New Genes Pop Up Like Magic

Since 2012 scientists have been learning how new genes are created in all kinds of organisms. The image below provides a look at simple gene expression, followed by a glimpse into the creation of a new gene out of “non-genic DNA.”

De Novo Genes
https://www.nature.com/articles/d41586-019-03061-x

It is a startling idea, and strangely liberating. The implications of this scientific revelation are likely to unfold in a disruptive manner, for decades to come at least.

In the past five years, researchers have found numerous signs of these newly minted ‘de novo’ genes in every lineage they have surveyed. These include model organisms such as fruit flies and mice, important crop plants and humans; some of the genes are expressed in brain and testicular tissue, others in various cancers.

… Conventional wisdom was that new genes tended to arise when existing ones are accidentally duplicated, blended with others or broken up, but some researchers now think that de novo genes could be quite common: some studies suggest at least one-tenth of genes could be made in this way; others estimate that more genes could emerge de novo than from gene duplication. Their existence blurs the boundaries of what constitutes a gene… __ https://www.nature.com/articles/d41586-019-03061-x

Evolution was once thought to be a slow and gradual process of mutation and selection. Then evidence of sudden bursts of evolutionary change was discovered, and more mechanisms of evolutionary change were found — such as gene duplication and recombination. Still, many weaknesses in specific areas of evolutionary theory by natural selection were pounced upon by sceptics.

Now with the discovery of the seemingly spontaneous emergence of “genes out of non-genes,” evolutionary theory is due for yet another renovation. This rocky road of observation – experimentation – theoretical emergence is how science is done. Scientists should be ever sceptical of “scientific” theories, especially those that are most cherished.

… only a few per cent of the human genome, for example, actually encodes genes. Alongside are substantial stretches of DNA — often labelled ‘junk DNA’ — that seem to lack any function. Some of these stretches share features with protein-coding genes without actually being genes themselves: for instance, they are littered with three-letter codons that could, in theory, tell the cell to translate the code into a protein.

It wasn’t until the twenty-first century that scientists began to see hints that non-coding sections of DNA could lead to new functional codes for proteins. As genetic sequencing advanced to the point that researchers could compare entire genomes of close relatives, they began to find evidence that genes could disappear rather quickly during evolution. That made them wonder whether genes could just as quickly spring into being. __ Nature

Genes must then appear and disappear with astounding regularity, and until recently we did not have a clue that this was happening. We knew that existing genes were turned on and off regularly, but not that new genes were being created from non-coding DNA and old genes were disappearing back into non-coding DNA.

One thing separating a “gene” from a “non-gene” in the DNA world, is the codons that tell the cell machinery to begin and end the translation process of DNA to a peptide, or chain of amino acids. Whether these new peptide sequences serve a useful purpose is up to the circumstances currently operating inside and outside of the organism itself. The new gene will be either “selected for” or “selected against” by all the working environments that interact with the gene product.

Start and Stop Codons
https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/codons_start_stop.html

Bacterial Resistance Easier to Understand

Knowledge of de novo genes suddenly opens a window into possible mechanisms by which bacteria quickly develop resistance to antibiotics. They do not have to “trade plasmids” with other bacteria. They can create their own brand-new resistance genes themselves!

A gene is commonly defined as a DNA or RNA sequence that codes for a functional molecule. The yeast genome, however, has hundreds of thousands of sequences, known as open reading frames (ORFs), that could theoretically be translated into proteins, but that geneticists assumed were either too short or looked too different from those in closely related organisms to have a probable function.

… Michael Knopp and his colleagues at Uppsala University, Sweden, showed that inserting and expressing randomly generated ORFs into Escherichia coli could enhance the bacterium’s resistance to antibiotics, with one sequence producing a peptide that increased resistance 48-fold7. Using a similar approach, Diethard Tautz and his team at the Max Planck Institute for Evolutionary Biology in Plön, Germany, showed that half of the sequences slowed the bacterium’s growth, and one-quarter seemed to speed it up8 — although that result is debated. Such studies suggest that peptides from random sequences can be surprisingly functional. __ Nature

And so we come back to the idea that challenges in the environment lead to evolutionary changes in organisms. The ability to create new genes and new proteins that can be tested by these environmental challenges would seem to provide a powerful new tool of evolutionary change. Especially in organisms with quick generation times such as bacteria.

For species such as humans who reproduce much more slowly, evolution via de novo genes seems to occur over much longer periods of time. But when smaller breeding populations are isolated from each other, rapid gene creation can occur and be selected for or against over shorter time periods — especially when the population is under challenge from the environment.

Gene Regulation
https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/gene_control.html

The story is more complicated than the discussion above suggests. Genes are also distinguished from non-genes by “regulatory regions” in the DNA which tell the cell machinery when to transcribe the gene to messenger RNA (mRNA), and then forward the mRNA to ribosomes for translation to peptides. The image above provides a simplified look at gene regulation. The image below is more realistic, but still is somewhat simplified.

https://en.wikipedia.org/wiki/File:Gene_structure_eukaryote_2_annotated.svg

So it obviously takes longer to cook up a set of “magical new genes” than to warm up a cold pizza in the microwave. Functioning genes in multi-cellular organisms — such as mammals — are a bit complicated when looked at with all of their regulatory control systems. Yet the existence of the de novo gene creation phenomenon seems to open an evolutionary doorway to us that we did not formerly know existed.

Non Coding DNA and RNA

Most of our DNA is “noncoding,” which means that most DNA either does nothing or it does other things besides functioning as genes. Much of it acts to regulate the expression of genes.

Similarly, our cells contain a large amount of non-coding RNA, much of it performing important tasks involving gene expression and important regulation of coding RNA. These are very active areas of research in molecular biology and genetics.

Most of What We Know, Just Ain’t So

If a scientist were able to travel back in time in the attempt to teach 19th century biologists what is now known by 21st century biologists, he would be taking a huge risk of being ridiculed and possibly attacked as heretics by any number of faiths that were prominent in that century, including “19th century science.”

The same thing will probably be true for 23rd century scientists who may risk their lives and limbs traveling back in time to our day. We are simply too early in this drama to know where it will end. We can be sure that we barely understand some of the surface layers.j

Hope for the best. Prepare for the worst. It is never too late to have a Dangerous Childhood © .