Californian two-spot octopus (Octopus bimaculoides). Embryo at the final stage before hatching. The species is named after the two prominent blue eyespots that can help deter predators.
How much new DNA does evolution need to produce a new biological capability? Intelligent design creationists commonly assume that new functions require new “complex specified information”, then insist that only an intelligent designer can supply it. But this overlooks something fundamental about genomes: what matters is not simply which genes an organism possesses, but how, where and when those genes are used. Rearranging existing components can change what a biological system does, without requiring every component to be invented afresh, and, importantly, no new DNA being inserted into the genome.
A new study published in Nature Communications explores this possibility in coleoid cephalopods — octopuses, squid and cuttlefish. These animals have elaborate nervous systems and remarkable behavioural capabilities. The research suggests that part of the explanation for their evolutionary innovations may lie in the three-dimensional organisation of their genomes.
DNA does not lie inside a cell as a neatly stretched-out sequence. It folds, bringing regions that are distant along a chromosome into physical proximity. Those contacts can influence gene regulation. An ancient episode of extensive genome rearrangement in the ancestors of coleoids created opportunities for previously separated regions to acquire new regulatory relationships. The researchers describe the resulting interdependence as “regulatory entanglement”.
Comparing genome organisation and gene activity across species, tissues and developmental stages, the team found a combination of stability and flexibility: larger chromatin domains were broadly conserved, while hundreds of smaller DNA loops varied with species and biological context. Their experiments also went beyond comparisons: deleting a candidate regulatory sequence using CRISPR–Cas9 demonstrated a role for these long-range interactions in neural development.
This is not proof that genome rearrangement alone produced cephalopod intelligence, nor does it mean that no new DNA evolved. The study also considers genome expansion. Its importance is more interesting than either oversimplification: evolutionary novelty can involve changes in the relationships between genetic components, as well as changes to the components themselves.
That leaves the intelligent design argument with a familiar problem. Calling a biological outcome “information” does not demonstrate that it required a supernatural author. Here, scientists are investigating physical mechanisms through which genome evolution can generate new regulatory possibilities. Whether creationists choose to call those possibilities “new information” changes neither the mechanisms nor the evidence. The scientific question is how complexity evolved — and this research offers another testable part of the answer.
Same Genes, Different Instructions^ How Genome Organisation Changes What Cells Do. A genome is more than a collection of genes. Its biological effects also depend on how those genes are controlled and how DNA is arranged inside the cell. Evolution can therefore modify an organism by changing the use of existing genes, as well as by changing their sequences or producing new copies.The paper in Nature Communications was announced by a news release from the University of Vienna:
Genes and their switches Protein-coding genes contain instructions for making proteins, but producing the right protein in the right place and at the right time requires regulation. Regulatory DNA sequences help control this process. These include promoters, where transcription begins, and enhancers, which can increase the activity of particular genes in suitable cellular conditions.
This distinction helps explain how cells with essentially the same genome can become such different things as nerve cells, muscle cells and skin cells. Much of the difference lies in which genes they express, and at what levels.
A genome has three dimensions Inside the nucleus, DNA is packaged with proteins into chromatin. This material folds into a complex, changing three-dimensional arrangement. Consequently, two sequences far apart along a chromosome can become neighbours in physical space.
Such folding can bring an enhancer close to a gene whose activity it influences. However, proximity alone does not guarantee regulation: the sequences involved, the proteins present and the cellular context also matter. DNA folding helps determine which interactions are possible.
What happens when DNA is rearranged? Chromosomal rearrangements can move, reverse or join stretches of DNA. A gene may consequently acquire a different regulatory neighbourhood, even if its protein-coding sequence remains unchanged. Existing regulatory elements can gain access to different targets, while established interactions may be weakened or lost.
Most importantly, a different pattern of gene expression can have a biological effect without requiring a wholly new protein. Changing when a developmental gene becomes active, where it acts or how much of its product is made can influence the development of tissues and organs. Such changes can be harmful, neutral or beneficial; rearrangement is not automatically an improvement.
Stability alongside evolutionary innovation In the cephalopod study, researchers found that larger chromatin domains were broadly conserved, whereas many finer-scale loops differed between species, tissues and developmental stages. They propose that genome rearrangement can establish new regulatory relationships which subsequently become interconnected — a process they call regulatory entanglement.
This offers a potential route to innovation while essential functions are retained. The work supports a role for long-range regulation in neural development, but does not establish that genome folding alone explains cephalopod intelligence.
Does this count as “new information”? DNA quantity, gene number and biological capability are not interchangeable measures. An organism need not acquire an entirely new set of genes every time evolution produces a new feature. Changes to the organisation and regulation of existing material can also produce new functional relationships.
Calling such a relationship “new information” does not explain its origin, still less demonstrate supernatural intervention. The useful scientific questions are specific: what changed, how did it affect gene activity, and what consequences followed? Those questions can be investigated experimentally. An assertion that “information requires a designer” cannot substitute for that investigation.
Brief glossary
- Gene expression
- The use of a gene’s DNA sequence to produce RNA and, for protein-coding genes, a protein.
- Chromatin
- DNA together with the proteins that package and organise it inside the cell.
- Enhancer
- A regulatory DNA sequence that can increase a target gene’s expression, sometimes acting over a considerable distance along a chromosome.
- Chromatin loop
- A folded arrangement that brings separated regions of chromatin into proximity.
- Chromatin domain
- A region within which chromatin tends to interact more frequently internally than with neighbouring regions.
- Regulatory entanglement
- The proposed development of interconnected regulatory relationships between genomic regions, potentially helping to preserve their association over evolutionary time.
3D structure of DNA may explain how cephalopods evolved complex brains
Octopuses, squid and cuttlefish, collectively known as coleoid cephalopods, have evolved exceptionally large and elaborately structured nervous systems capable of complex behaviours such as problem-solving and rapid camouflage. A new study by scientists at The University of Vienna suggests that the origins of this complexity may lie not just in the genes themselves, but in how the genome is organised in 3D. The researchers found that ancient, extensive reorganisation of the genome altered how DNA is arranged inside the cell. These shifts brought previously distant regions of DNA into contact, changing the way genes are regulated. Understanding this process could change how we think about how new traits emerge during evolution. The findings are currently published in the renowned journal Nature Communications.
The team studied the 3D structure of the genome across octopus, squid and cuttlefish, combining data on DNA structure with gene activity.
The genome isn't just a sequence of genes. It's folded into a complex three-dimensional structure. Understanding how that structure evolves is becoming increasingly important for understanding how new forms of biological complexity arise.
Dr Thea M. Rogers, lead author
Department of Neuroscience and Developmental Biology
Division of Molecular Evolution and Development
University of Vienna
Vienna, Austria.
"Regulatory entanglement" as a consequence of genome reorganisation
In cephalopods, a large-scale burst of genome reorganisation, which occurred hundreds of millions of years ago, dramatically reshuffled the genome and brought previously distant regions of chromosomes into close proximity.
The researchers found that when regions of DNA are brought into contact, they can begin to interact and influence each other's activity. Over time, these interactions can become embedded, forming increasingly interconnected regulatory networks.
"Regulatory entanglement" balances innovation and stability in genome evolution
This process, described by the researchers as "regulatory entanglement", may allow genomes to generate new patterns of gene expression while maintaining essential functions.
Not all aspects of genome structure appear to respond to genome reorganisation in the same way. The researchers found that large structural units of the genome, known as chromatin domains, remained largely stable over evolutionary time.
In contrast, finer-scale connections known as chromatin loops were far more dynamic. These loops bring distant regions of DNA into contact. They varied widely across species, tissues and developmental stages, and were often found near genes involved in key cephalopod traits, including those linked to the nervous system. This suggests that these more flexible regions may be particularly affected by large-scale changes in DNA organisation.
3D structure of DNA shapes evolutionary processes actively.
Together, these findings challenge the idea that genome architecture is a passive consequence of evolution. Instead, they suggest that the 3D organisation of DNA actively shapes how evolution unfolds. In cephalopods, this may have played a key role in the emergence of their unusually complex nervous systems.
Summary
- Scientists at the University of Vienna reconstructed the 3D organisation of the genome in octopus, squid and cuttlefish to investigate how genome architecture evolved following an ancient burst of genome reorganisation.
- The study found that this large-scale reorganisation brought previously distant regions of DNA into contact, creating new networks of regulatory interactions that became embedded over evolutionary time.
- The researchers describe this process as "regulatory entanglement", whereby new DNA interactions become increasingly interconnected, allowing genomes to generate novel patterns of gene regulation while maintaining essential biological functions.
- The researchers found that not all aspects of the 3D genome respond to genome reorganisation in the same way. Large chromatin domains remained remarkably stable, whereas finer-scale chromatin loops were far more dynamic.
- The findings challenge the view of genome architecture as a passive consequence of evolution and instead suggest that the 3D organisation of DNA can actively influence evolutionary change.
Publication:
What makes this research significant is that it reveals another way in which evolution can generate biological novelty: by changing the relationships between genetic components. A genome is not merely a list of protein recipes. Its organisation helps determine how those recipes are used, and rearranging existing DNA can create opportunities for new patterns of regulation. The researchers have identified a mechanism that may have contributed to the evolution of the elaborate nervous systems of octopuses, squid and cuttlefish, without pretending that this alone explains their intelligence.
For intelligent design creationism, the difficulty is not resolved by attaching the label “complex specified information” to the outcome. If altered regulatory relationships count as new information, then the question becomes how those relationships arose — precisely the sort of question evolutionary biology investigates. If creationists decline to call them new information, they must acknowledge that important functional changes can arise through the reorganisation of existing material. Neither choice establishes a need for supernatural intervention.
Nor does the study suggest that evolution has run into an explanatory barrier. Evolutionary history provides the framework for comparing these genomes, identifying conserved interactions and investigating how new ones emerged. The remaining uncertainties are questions for further research, not evidence of a designer. Once again, science advances by examining what nature actually does, while the creationist objection depends on insisting that natural processes cannot do what the evidence increasingly helps us understand.
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