Scientists Propose Novel Theory on Origin of Genetic Code
Alan Herbert, Scientific Supervisor of the HSE International Laboratory of Bioinformatics, has put forward a new explanation for one of biology's enduring mysteries—the origin of the genetic code. According to his publication in Biology Letters, the contemporary genetic code may have originated from self-organising molecular complexes known as ‘tinkers.’ The author presents this novel hypothesis based on an analysis of secondary DNA structures using the AlphaFold 3 neural network.
The genetic code is the 'alphabet' that underpins the functioning of all living systems on Earth. It dictates the content of an organism's 'instructions' and how they should be interpreted. The contemporary genetic code is composed of codons, each consisting of three nucleotides. These triplets encode amino acids, which are then involved in protein synthesis. Scientists have been studying the genetic code for over 70 years, yet one of the most important questions—how it originated—remains unanswered.
Professor Alan Herbert, Scientific Supervisor at the HSE International Laboratory of Bioinformatics, has put forward a new explanation for the origin of the genetic code. In his view, during evolution, flipons—DNA sequences capable of forming secondary structures—played a key role in the development of the contemporary genetic code.
The classical DNA molecule, as described by Francis Crick and James Watson, is a double helix that twists to the right. However, scientists have discovered alternative DNA structures, including Z-DNA, which twists to the left, as well as three-stranded and four-stranded sequences, and knot-like DNA structures known as i-motifs. These unusual structures arise under specific physiological conditions, and their type depends on the sequence and arrangement of nucleotides within the flipon itself. The simplest flipons are formed from repeating nucleotide sequences, leading to the assumption that such sequences were abundant in the so-called primordial soup.
Maria Poptsova
Using DeepMind's AlphaFold 3 neural network, Alan Herbert analysed the nature of the bonds between flipons and amino acids. 'It turns out that flipons formed from two-nucleotide repeats bind very effectively to simple peptides composed of two-amino acid repeats. It is precisely this correspondence that exists in the contemporary genetic code,' comments Maria Poptsova, Head of the HSE International Laboratory of Bioinformatics.
For example, the cytosine-guanine repeat CGCGCG forms Z-DNA, and the peptide with the arginine-alanine repeat RARARA binds effectively to this sequence. In the contemporary genetic code, the CGC codon corresponds to arginine, while the GCG codon corresponds to alanine. A detailed analysis of spatial interactions reveals that the strongest connection occurs between non-overlapping triplets: CGCGCG binds to RA.
In his publication, Alan Herbert examines numerous examples of the interaction between flipons formed from short repeats and peptides made up of amino acid repeats. It has been found that reactions leading to mutual chain elongation can also occur, especially in the presence of magnesium and zinc, which act as catalysts.
According to the study author, such complexes were once formed by special components—tinkers, as François Jacob called them. In Professor Herbert's work, structures composed of flipons and peptides serve as self-replicating tinkers. Tinkers used DNA as a template for protein synthesis, while proteins, in turn, facilitated the elongation of the DNA helix. As a result, a non-overlapping triplet code emerged: the odd number of bases enables the encoding of sequences from different amino acids, while the nature of bonds between flipons and amino acids dictates that each codon corresponds to only one amino acid.
'The role of flipons as tinkers in the early stages of biological evolution offers a radically new perspective on the origins of life. It is no exaggeration to say that if this theory is experimentally confirmed, our colleague Dr Herbert deserves the Nobel Prize,' explains Poptsova. 'The discovery of interactions between flipons and amino acids, in accordance with the contemporary genetic code table, proves that the emergence of the genetic code is not an accident but a natural outcome of evolution. Nature does not create anything from scratch; it develops new mechanisms using what is already available. Nature acts like a tinkerer who, when needing to quickly create something functional—but not necessarily reliable or durable—grabs whatever is at hand.'
Alan Herbert
'Overall, the proposed scheme does not require a DNA, RNA, or peptide world to explain life’s origins,' writes Alan Herbert in his article. 'Instead, the tinkers described are agents that promote this eventuality. They arise from the simple match between low-complexity nucleotide and simple peptide polymers, using metals to catalyse their initial replication. By spiking the prebiotic soup with copies of themselves, these tinkers quite naturally evolved a non-overlapping, triplet genetic code.'
In addition to advancing our understanding of life's origins, studying tinkers could lead to the development of new technologies, including artificial self-organising systems and self-healing materials. The tinkers’ ability to combine various chemical elements can be used for directed evolution of new biomolecules.
See also:
Mortgage and Demography: HSE Scientists Reveal How Mortgage Debt Shapes Family Priorities
Having a mortgage increases the likelihood that a Russian family will plan to have a child within the next three years by 39 percentage points. This is the conclusion of a study by Prof. Elena Vakulenko and doctoral student Rufina Evgrafova from the HSE Faculty of Economic Sciences. The authors emphasise that this effect is most pronounced among women, people under 36, and those without children. The study findings have been published in Voprosy Ekonomiki.
Scientists Discover How Correlated Disorder Boosts Superconductivity
Superconductivity is a unique state of matter in which electric current flows without any energy loss. In materials with defects, it typically emerges at very low temperatures and develops in several stages. An international team of scientists, including physicists from HSE MIEM, has demonstrated that when defects within a material are arranged in a specific pattern rather than randomly, superconductivity can occur at a higher temperature and extend throughout the entire material. This discovery could help develop superconductors that operate without the need for extreme cooling. The study has been published in Physical Review B.
Scientists Develop New Method to Detect Motor Disorders Using 3D Objects
Researchers at HSE University have developed a new methodological approach to studying motor planning and execution. By using 3D-printed objects and an infrared tracking system, they demonstrated that the brain initiates the planning process even before movement begins. This approach may eventually aid in the assessment and treatment of patients with neurodegenerative diseases such as Parkinson’s. The paper has been published in Frontiers in Human Neuroscience.
Civic Identity Helps Russians Maintain Mental Health During Sanctions
Researchers at HSE University have found that identifying with one’s country can support psychological coping during difficult times, particularly when individuals reframe the situation or draw on spiritual and cultural values. Reframing in particular can help alleviate symptoms of depression. The study has been published in Journal of Community Psychology.
Scientists Clarify How the Brain Memorises and Recalls Information
An international team, including scientists from HSE University, has demonstrated for the first time that the anterior and posterior portions of the human hippocampus have distinct roles in associative memory. Using stereo-EEG recordings, the researchers found that the rostral (anterior) portion of the human hippocampus is activated during encoding and object recognition, while the caudal (posterior) portion is involved in associative recall, restoring connections between the object and its context. These findings contribute to our understanding of the structure of human memory and may inform clinical practice. A paper with the study findings has been published in Frontiers in Human Neuroscience.
Researchers Examine Student Care Culture in Small Russian Universities
Researchers from the HSE Institute of Education conducted a sociological study at four small, non-selective universities and revealed, based on 135 interviews, the dual nature of student care at such institutions: a combination of genuine support with continuous supervision, reminiscent of parental care. This study offers the first in-depth look at how formal and informal student care practices are intertwined in the post-Soviet educational context. The study has been published in the British Journal of Sociology of Education.
AI Can Predict Student Academic Performance Based on Social Media Subscriptions
A team of Russian researchers, including scientists from HSE University, used AI to analyse 4,500 students’ subscriptions to VK social media communities. The study found that algorithms can accurately identify both high-performing students and those struggling with their studies. The paper has been published in IEEE Access.
HSE Scientists: Social Cues in News Interfaces Build Online Trust
Researchers from the HSE Laboratory for Cognitive Psychology of Digital Interface Users have discovered how social cues in the design of news websites—such as reader comments, the number of reposts, or the author’s name—can help build user trust. An experiment with 137 volunteers showed that such interface elements make a website appear more trustworthy and persuasive to users, with the strongest cue being links to the media’s social networks. The study's findings have been published in Human-Computer Interaction.
Immune System Error: How Antibodies in Multiple Sclerosis Mistake Their Targets
Researchers at HSE University and the Institute of Bioorganic Chemistry of the Russian Academy of Sciences (IBCh RAS) have studied how the immune system functions in multiple sclerosis (MS), a disease in which the body's own antibodies attack its nerve fibres. By comparing blood samples from MS patients and healthy individuals, scientists have discovered that the immune system in MS patients can mistake viral proteins for those of nerve cells. Several key proteins have also been identified that could serve as new biomarkers for the disease and aid in its diagnosis. The study has been published in Frontiers in Immunology. The research was conducted with support from the Russian Science Foundation.
Scientists Develop Effective Microlasers as Small as a Speck of Dust
Researchers at HSE University–St Petersburg have discovered a way to create effective microlasers with diameters as small as 5 to 8 micrometres. They operate at room temperature, require no cooling, and can be integrated into microchips. The scientists relied on the whispering gallery effect to trap light and used buffer layers to reduce energy leakage and stress. This approach holds promise for integrating lasers into microchips, sensors, and quantum technologies. The study has been published in Technical Physics Letters.