Most of Human Genome Nonfunctional: Study

An estimate derived from fertility rates concludes that at least 75 percent of our DNA has no critical utility.

By | July 17, 2017

ISTOCK, SUPPARSORNUp to 25 percent of the human genome is critical, while the rest has no function, according to a study published July 11 in Genome Biology and Evolution. The estimate, generated by looking at fertility rates and the expected frequency of deleterious mutations, contradicts a 2012 claim from a large international group called ENCODE, which estimated that 80 percent of the genome is functional.

“For 80% of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce,” writes Dan Graur, an evolutionary biologist at the University of Houston, in his study.

Graur’s model is built on the idea that fertility rates reflect how much of the human genome is vulnerable to deleterious mutations, and therefore functional. If most of the genome is functional, then people would have to have a lot of babies to maintain the human population and make up for the decreased chances of survival that accompany a greater possibility for harmful mutations. If only a small bit of the genome is functional, then the odds of a mutation taking out an important sequence are smaller, and therefore fertility rates can be lower.

Given that fertility rates have hovered around two to three children per couple for centuries, Graur instead looked at how much of the genome is functional with each person having 1.8 children on average. He finds 25 percent is the upper limit of functionality, with the actual number likely closer to 10-15 percent.

See “Getting to Know the Genome

As New Scientist points out, “functional” DNA is ill-defined, with ENCODE using a more liberal definition, while Graur restricts it to sequences subject to the possibility of deleterious mutations.

Ryan Gregory of the University of Guelph tells New Scientist that some sequences of DNA—and it’s unclear how many—may still be useful even though they may not be affected by mutations. Still, he adds, “I would like to think that most knowledgeable biologists who properly appreciate evolutionary theory and genomic diversity are well aware of the many problems with ENCODE’s claim.” 

Editor's note (July 18): We replaced the image after a reader pointed out that the DNA art had too many base pairs per twist of the double helix.

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Avatar of: PastToTheFuture

PastToTheFuture

Posts: 94

July 18, 2017

This is an excellent consideration of an important problem, but I have a serious problem with one assertion

---Given that fertility rates have hovered around two to three children per couple for centuries, Graur instead looked at how much of the genome is functional with each person having 1.8 children on average.---

I have to be very skeptical of those numbers. Then they should also be able to provide the rate of natural selection. Where is it? I expect it to be in the range of 50% at least. Is that fertility rate after natural selection? If so, it would hugely effect that percentage of functionality. Heck, also, not all mutations are lethal. Everyone has a few thousand single point mutations. With all respect, I'm skeptical.

If you want to read a consideration of this, see "Genetics For A New Human Ecology", which by the way suggests an excellent doctorate thesis idea of measuring  the incidence of de novo mutations and their consequence.

Avatar of: James V. Kohl

James V. Kohl

Posts: 443

July 18, 2017

If only a small bit of the genome is functional, then the odds of a mutation taking out an important sequence are smaller, and therefore fertility rates can be lower.

That conclusion makes sense in the context of natural selection for food energy-dependent codon optimality, which biophysically constrains RNA-mediated protein folding chemistry.  Feedback loops link the physiology of pheromone-controlled reproduction to protection from the virus-driven degradation of messenger RNA.

Simply put, the structure of functional DNA is food energy-dependent because what organisms eat prevents virus-driven entropy of their organized genomes in the context of reproduction.



I would like to think that most knowledgeable biologists who properly appreciate evolutionary theory and genomic diversity are well aware of the many problems with ENCODE’s claim.



Anyone who is not aware of the problems should search PubMed for the term "microRNA" before release of the cell biology game "Cytosis" forces them to learn what anyone more than ten years old can learn from playing the game.

Energy-dependent viral latency is biophysically constrained in organized genomes. Nutrient stress and social stress break the constraints and the stress-linked degradation of messenger RNA links viruses to all pathology.

Avatar of: BartT

BartT

Posts: 2

July 18, 2017

Heard this one before.  Remember the discovery of "junk DNA".  Well, we now know that the junk is actually useful.  The issue is not that so much of our DNA is not in play, it is that we are still not smart enough to understand how DNA works.

Avatar of: BartT

BartT

Posts: 2

July 18, 2017

Heard this one before.  Remember the discovery of "junk DNA".  Well, we now know that the junk is actually useful.  The issue is not that so much of our DNA is not in play, it is that we are still not smart enough to understand how DNA works and have not figured out what the rest of the DNA does.

Avatar of: Barry@DataSense

Barry@DataSense

Posts: 21

July 18, 2017

One can only conclude that the mathematical model underlying this study is flawed. I find it hard to accept that 'nature' (evolution) is so inneficient.

As an analogous argument, a birds wing bones are 5 times as strong as they need to be for normal flight - does that mean that 80% of the bones' strength is 'wasted'?

Avatar of: James V. Kohl

James V. Kohl

Posts: 443

Replied to a comment from BartT made on July 18, 2017

July 18, 2017

Supercoiled DNA is energy-dependent. The energy comes from food. What is not understood about that fact?

Food energy Richard Feynman complains about all the different units that are used to measure the single concept of Energy.

 

Avatar of: James V. Kohl

James V. Kohl

Posts: 443

Replied to a comment from James V. Kohl made on July 18, 2017

July 19, 2017

For an example of the glaring flaw in mathematical models, see: Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition was reported as: Epigenetics between the generations: Researchers prove that we inherit more than just genes

It has been long debated if epigenetic modifications accumulated throughout the entire life can cross the border of generations and be inherited to children or even grand children.

That is a lie! The debate ended several decades ago.


See: From Fertilization to Adult Sexual Behavior


We included a section on molecular epigenetics that can be linked to Richard Feynmans's example of human idiocy in the context of food energy. He linked the theft of quantized energy from the radiation-driven viral degradation of messenger RNA to amino acid substitutions in viruses.


The amino acid substitutions in the viruses have been placed into the context of energy-dependent changes in base pairs and beneficial mutations by all biologically uniformed theorists.


Pseudoscientists still claim that mutated viruses cause natural selection and the evolution of one species to another.  That's why they use terms like enhancers in the context of their ridiculous mathematical models.


The models of biologically uninformed pseudoscientists eliminate energy-dependent changes in base pairs and changes in the microRNA/messenger RNA balance from consideration.


For comparison, more than 62,000 published works link changes in the de novo creation of plant and animal microRNAs from chirality and autophagy to healthy longevity. The changes also link virus-driven energy theft from the degradation of messenger RNA to all pathology in all living genera.


Feynman placed that fact into the context of a lecture and he included a segment on food energy. He claimed that using different measurements and terms in the context of energy exemplifies human idiocy.  The ambiguity of the term "enhancers" is an even better example.

Avatar of: M3

M3

Posts: 1

July 19, 2017

Bird bones are simple, just like airplanes: normal flight can involve high loads, for example wind gusts and turbulence, as well as "high g" deliberate maneuvers.

Avatar of: LHADJI

LHADJI

Posts: 1

July 21, 2017

Some time ago, some idiot(s) had coined the "stupid" word "Junk DNA" out of total IGNORANCE about its utter usefulness and possible function in gene function and expression......and a lot of scientists use that stupid expression in countless research and review articles. At one science meeting I asked the speaker if he could build a house by beginning with the roof!!no comments on his ignorant silence; then I asked him if he had any sound evidence that what he called "Junk DNA" is in fact "Junk DNA"? No comment either!!! A lot of scientist follow the ignorant and fashionable herd of uncultured and unintelligent (no deep-thinkers at all) scientists. A good scientist should show evidence or a sound theory justifying his ascertions. I could give a lot of such examples of meanigless wqrds or expression coinedor false or fake ideas promoted by scientists in need of "recognition"!!! Before asserting something in REAL SCIENCE, facts, proof and sound theories should be put forward for colleagues to judge and estimate.

Avatar of: James V. Kohl

James V. Kohl

Posts: 443

Replied to a comment from LHADJI made on July 21, 2017

July 22, 2017

Olfaction Warps Visual Time Perception

The obvious link from food energy as quantized information that is biophysically constrained in organized genomes via the physiology of pheromone-controlled reproduction, which links amino acid substitutions from supercoiled DNA to protection from the virus-driven degradation of messenger RNA, has been placed into its proper context during the past 50 years. But pseudoscientists still prefer their ridiculous theories that link mutations to evolution.

Junk DNA was invented to obfuscate facts about supercoiled DNA that link energy-dependent changes in base pairs to all biodiversity and virus-driven energy theft to all pathology.

 

 

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