Conceptual and empirical challenges of ascribing functions to transposable elements

Area of Science:

• Philosophy of Science
• Genomics
• Evolutionary Biology

Background:

• The Encyclopedia of DNA Elements (ENCODE) project claimed 80% of the human genome has biochemical function, sparking scientific debate.
• Discussions around genome function often lack clear conceptual frameworks.

Purpose of the Study:

• To clarify biological function concepts relevant to genomics research.
• To analyze the ENCODE project's claims using philosophical concepts of function.
• To highlight challenges in defining function for transposable elements.

Main Methods:

• Review of philosophical concepts of biological function: causal role and selected effects.
• Analysis of the ENCODE project's methodology and claims through these lenses.
• Identification of specific issues related to transposable elements (TEs).

Main Results:

• The ENCODE project's claims are problematic due to the misuse of the causal role concept of function, not its adoption.
• Transposable elements (TEs) present unique challenges for function attribution, including selection levels and origin vs. persistence.
• Accidental vs. functional benefits and organism-level selection require careful consideration for TEs.

Conclusions:

• A clear understanding of function concepts is crucial for interpreting large-scale genomic data.
• ENCODE's broad claims about genome function, particularly concerning TEs, require more nuanced philosophical and biological scrutiny.
• Future studies on eukaryotic genome function must address TE-specific challenges and evolutionary dynamics.