Collapse of the Junk-DNA theory will destroy the theory of evolution

Without genomic junk, mutational load will drive species into extinction

As we already know, there are only about 19'000 DNA sequences used for protein encoding in the human genome.  It is less than in one of the smallest multicellular organisms, C. Elegans (length ~1 mm). According to the most recent studies, different proteins in our body are up to six million. Are there areas in the DNA that control how the cell reads the sequences used for protein encoding?

The ENCODE project in 2008-2102 systematically mapped the entire human genome in terms of transcription, transcription factors, chromatin structure, and histone modifications. The project discovered that 80.4% of our genome is biochemically active and functional especially outside of the protein coding sequences.
 

Despite functionality for such a large share of DNA was found, leading evolutionary biologists did not agree to believe that this part would be beneficial. For example, PZ Myers in several of his writings belittles the results of the ENCODE project.

Later research has discovered how cells use the non-coding region for many different purposes:

1. Dr. John Stamatoyannopoulos from the University of Washington states that Encode revealed 40 million different switches (epigenetic switches) in our genome that control and regulate these genes (protein coding sequences). According to the researchers, the area found by ENCODE is a kind of operating system. It is therefore clearly both useful and functional, and in no case any junk or useless filling.

2. The ENCODE project didn't discover how the cell uses the so-called STRs (Short Tandem Repeat) sections. These are short repeating DNA sequences that appear more like typing errors or noise. However, researchers have found that STR sequences are very important regulatory elements in our genome and affect about 10-15% of human phenotypical differences (their methylation levels).

3. Transposable elements (LINEs, SINEs, ERVs and DNA transposons) have all been found to be very important and useful. They have several different tasks. By reading them, cells typically construct non-coding RNA molecules, such as lncRNA, microRNA, siRNA, and PiRNA molecules.

4. Heterochromatin is tightly packed DNA in the chromosome. It has only recently been discovered that cellular mechanisms recruit 'ambulances', i.e. two-legged myosin engine proteins, to transport damaged DNA sequences in heterochromatin to be repaired at the nuclear pore complex. So the cell is also trying to fix faulty DNA.

Conclusion: The cell is capable of modifying DNA in many ways, either by combining sequences or by repairing already damaged strands. DNA is a passive data resource for the cell that it uses to build functional RNA molecules. Due to the passive role of DNA, there is no unnecessary or filling DNA in the cell, but everything is useful. It is a data warehouse, a pool from which the cell searches for appropriate sequences for different purposes using highly sophisticated guiding and control mechanisms.

Mutational load is so high that the cell is not able to correct all errors. Disruptions in the epigenetic mechanisms and impaired performance result in the cell being unable to re-organize the damaged DNA at the ends of the chromosomes in telomeres. This is why chromosomes are combined and their total count decreases.

In our own lifetime, it’s estimated that 40,000 species become extinct every year.