Human genomics

The new world of DNA

A long-term effort to catalogue all the bits of the human genome that do something has released its results

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The concept of adaptive evolution requires selection for nutrient chemicals and species-specific mixtures of chemicals called pheromones in species from microbes to man. Simply put, new chemical activity in the cell must trigger a fairly powerful selective force. Nutrient chemicals and pheromones cause receptor-mediated chemical activity in the cell that triggers natural selection, which is a powerful selective force.

A plagiarist addressed this concept, when he wrote:“... I envision some unconditioned stimuli to have been such a prevalent and regular feature of past environments that it makes sense to bypass the normal learning mechanism and encode the process in the DNA.” Nutrient chemicals and pheromones are prevalent unconditioned stimuli and they are also regular features of all past environments that encode normal receptor-mediated learning mechanisms in the cell via the chemical activity that causes natural selection, which is a powerful selective force.

Unfortunately, few people seem to understand my conceptualization of how organisms are epigenetically fed the nutrient chemicals that enable gene duplication as a mechanism of genomic adaptation to a changing environment. "Epigenetically fed” does not mean that DNA from one species becomes functional as DNA in another. Instead, receptor-mediated ingestion of heterospecific DNA is the nutrient chemical that enables gene duplication in conspecifics. The gene duplication is required for adaptive evolution via ecological, social, neurogenic, and socio-cognitive niche construction in species from microbes to man.

As an alternative to my model of detailed adaptive evolution, one of the people involved in presenting the ENCODE data has said there are “random models” that may explain adaptive evolution across species. Does anyone know what he’s talking about? What “random model” helps to explain the species diversity that results from nutrient acquisition and the metabolism of nutrient chemicals to pheromones, which control reproduction in all species?

If there is a “random model” that has any explanatory power not why haven’t the details of the model been offered for consideration. The “random models” proposal makes me think we will continue to be misled about the requirements for selection in the context of epigenetically altered cause and effect that involves the complexity of the genome and natural selection in all species. Will the ENCODE groups ever look at how nutrient chemicals and pheromones epigenetically effect intracellular signaling and stochastic gene expression in an attempt to determine what chemicals cause cells to differentiate, species to speciate, and some people to realize that nutrient chemical driven gene duplication and the constraints of pheromones that control reproduction represent the pattern of biological design that can be followed across species?

"Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans." Kohl (2012)


We need to get more Engineers into projects like this, I'm fed up of the "shock" of Biologists to things that seem obvious to a designer. A manufacturing machine has a huge control systems even for a fairly simple machine tool, our cells must need a lot of control system to know what to produce, when and how much, where to send it and how to fold the proteins etc. Its no surprise that most of the gene is regulatory. There is clearly also a lot of error correction that will use quite a lot of genome bases.
I would also predict that a large proportion of the genome that they haven't found out what it does will be associated with the developmental stage. Building a factory takes a lot of information as well as running it. Evolutionary assumptions of this being built by random mutation has really harmed our understanding and research attempts, for years the "Junk" idea stopped us even looking at non coding regions yet from an engineering view there had to be the control circuits somewhere.


Good article. I wonder if such a consortium will ever be able to figure out our way into regenerative organs.

Kevin Viel

'Still, it seemed as if only a small fraction of the genome was actually doing anything, and that a lot of the rest was, or might as well be, “junk”.'

This seems to be a canned, press release-like mainstay of the reports on this project. It seemed unlikely that this vast amount of DNA served no purpose. To replicate and transcribe DNA cost energy, in the case of transcription, I believe that it is one ATP per nucleotide. Further, it is "slow; again in the case of transcription, about 10-15 nucleotides per second, thus requiring about 3 hours to transcribe the 186 Kb F8 gene, for instance. Lastly, DNA is highly coiled, and the uncoiling, the binding of machinery (molecules and complexes) through collision, and use of DNA is essentially random, although the impressive machinery puts the odds highly in favor of the actions. An analogy might be the way activated platelets provide a surface for some of the coagulation reactions, thereby taking a 3D environment and making it 2D and making the reactions more likely (rapid-essential to prevent exsanguination). Had this DNA been "junk", the cells and organisms that lack some of it might have had an advantage; namely, reproducing and processing DNA with less energy and complexity. Indeed, not likely to be junk.


To a large extent public perceptions and expectations are sculpted by media reports in print, web, and tv. The shallow nature of the vast majority of reports leaves us with a poor understanding or even outright misconceptions regarding these kinds of complex topics. I suppose this is because "reporters" and writers are not well versed in science. I don't think they do it on purpose; they just don't know any better.

I don't think The Economist intends to be a scientific journal, so if you want to understand a technical topic you have to do some research on the topic elsewhere, which is as it should be.
Perhaps The Economist could provide web links or contact info for those who wish to do additional reading on a technical topic.

I appreciated the article very much.

Moran ya Simba

"So, for example, a number of sites in the genome that appear relevant to Crohn’s disease—an inflammation of the digestive tract—are not associated with any known protein-making gene. But the parts list says those regions contain, or are close to, a particular kind of genetic switch turned on and off in various types of immune cell."

Wow. The idea that DNA was simply a long string of recipes for proteins was always too simplistic. There is a very complex interaction between proteins, RNA and DNA. I think there are even new families of molecules central to these networks.


As a scientist and cartoonist, I cant say "Junk". There is no such a thing in the nature that we can call junk. Just because of we don’t get it yet…we don’t have the right to call junk, thrash…etc.
I would like to contribute to the article with one of my cartoons at Biocomicals which is related to the topic;

Vargha in reply to biocomicals

junk DNA in biology just means it doesnt have vital functions in the dogma of molecular biology, meaning it doesnt transcribed and translated, much like the function of spectator ion in chemistry.


I was surprised to not see a reference to cancer treatment in this Economics based magazine. If it is willing to discuss DNA as a part of economics; shouldn't it relate it to the biggest economic destruction factor of so many families: The medical care costs of cancer treatment?


It appears that not only brain resembles a (very complex and complicated) computer, but also organs, tissues and even cells have control systems with lots of switches and sequences of their operations.DNA is a basic hardware.

maybury in reply to guest-iosomnj

I would agree, but I think it slightly more accurate to say "computers resemble our brains/tissue systems" and that DNA is software that has the information to build its on hardware! mind boggling.

I wish my computer could build itself or repair its own components.


Fascinating. Yet, I was wondering how ENCODE aligns with the cover story from a few weeks ago - 'Microbes maketh man'. Does the ENCODE contain genome for the microbes that live in our bodies too? Don't think so! It would be interesting to see how the microbial genome across humanity looks like.


Seven years ago, when I was working at an NIH-funded research institute, I happened to mention to one of the Principal Investigators (who was working on gene expression profiles) that it seemed from an evolutionary perspective quite odd to imagine that the vast majority of a person's DNA was merely non-functional "junk." I reasoned that copying sequences takes energy, and nature is pretty parsimonious over long periods of time. Surely any true "junk" would tend to drop out of the genome over time? I was told, curtly, that obviously I didn't understand how genetics worked.

Nice to see that once again, thinking about things from first principles can sometimes lead to clarity and that "experts" too often get lost in the weeds.

teacup775 in reply to CA-Oxonian

True. And the whole idea that something as complicated as a living organism never would have evolved control code for its functional repetiore hard to believe. The real world sculps engineering principals.

But Nature doesn't bother too much with code comments or documentation. I think.

Reido in reply to CA-Oxonian

From an evolutionary perspective, it's quite reasonable for significant "junk" to accumulate: evolution hasn't eliminated vestigial parts from the gross anatomy of organisms. The question is whether losing junk is enough of a gain in response to the pressure of selection. Given the absolute importance of preserving (most of) the genome intact, dutiful copies of even the junk could be more valuable than a hypothetical copying mechanism that is more open to speculative elimination of entire sections.

But on the other hand, evolution is also improvisational to an astounding degree. If there are some unused bits lying around, then evolution tends to tweak and thereby find a use. So based on that, evolution doesn't typically keep around a lot of junk.

Photo-punk in reply to CA-Oxonian

I'm an interested layperson and believed the same thing as CA-Oxonian (and still do, since evidence has born me out). This is what I love about Science: there is always room to question current dogma because the ultimate arbiter of truth is Nature herself.

I'm glad that I live in a culture where I can indulge my view that you should not trust a self-described expert more than you trust anyone else. The wise man is he that knows he knows nothing.

supamark in reply to Reido

About the only evolutionary advantage I can see from having a lot of actual junk DNA is that it could reduce errors in coding genes. Every time a cell divides and the DNA is copied, 2 or 3 errors (mutations) are introduced. Having a lot of junk DNA would mean the junk is more likely than the coding portions to mutate, and mutations in actual junk DNA would not be harmful.

maybury in reply to supamark

except that the errors happen in the form of one error per billion bases, so if youjust add a few billion bases of junk you don't reduce the number of errors in the bit you care about. photocopying several sheets of old newsprint doesn't improve the quality of the photocopy of your treasured document.

maybury in reply to Reido

What "Vestigial" organs are left? The appendix is a test tube for our immune system, our coccyx is an important muscle attachment point, what organs are left that are vestigial, there are ones we can live without but I know of none that are vestigial?

supamark in reply to maybury

There's only about 3 billion base pairs in all our chromosomes combined. If most of that were actually junk, then the 2 to 3 mutations per cell division would in fact be more likely to occur in a non-coding region. It isn't junk like previously thought though.


Junk DNA? Wasn't that science settled, too?

Philipp.JFR in reply to bampbs

No, they're more commonly referred to as non-coding DNA segments and we've known that at least some of them do something for a long time now, we just didn't know what.
Also, there's no such thing as settled science, only varying levels of empirical data from which we can extrapolate confidence in our understanding.

Terence Hale

The new world of DNA. The anatomy of a mess. Trying with my limited resources to figure out this strange world of DNA signals I have adopted a poor man approach. Unlike the big guys I just convert the nuclide sequences to pictures looking for a “Da Vinci Code”. At the moment I have to buy a new hard disk but I think there something in it.

Connect The Dots

It was naive to believe a decade ago when the human genome was completely sequenced, that we would shortly have a competent tool to manipulate genes, cure disease and change the evolution of man.

Some parents optimistically reckoned they would have a catalogue to dial in their offspring's height, hair color, eyes, intelligence, thinness, longevity, and personality within a generation.

And hard living, vodka drinking, chain smoking, drug abusing, all-you-can-eat, morbidly obese slobs, thought that gene manipulation would produce a panacea pill that would enable them to live to 100 years and still remain on the couch watching TV.

Gene therapy has not cured any patient.
And has caused more deaths than prevented.

The promise is still ethereal.

Nature's clockwork is far more complex.

...Yet it is light years more practical and promises more benefits than let say Higgs-Boson God-Particle Research. CUT that funding and spend a fraction of that on better Sci-Fi Films that take us to the edge of the universe but do not waste billions in rocket fuel.


The Encode project is a start in providing insight into how our DNA works, but early findings will renew hopes for personalised medicine. Understanding better how DNA/RNA influences common diseases is a major step forward.

When the human genome was sequenced a decade ago scientists knew their discovery was just a start; large parts of the DNA blueprint that was laid bare and how it functions has largely remained a mystery. Understanding the endless loops and lengths of DNA inside our cells, and what they are up to, will revolutionise science and medicine in the years and decades ahead.

ENCODE does much more than provide a straightforward list of genes. By creating a complicated database and catalogue of all the places along our DNA strands that are biochemically active, they offer new insight into how genes work, replicate and influence common diseases. The research also upends the conventional wisdom that most of our DNA serves no useful purpose, a point borne out by this excellent article from The Economist.

Defining this hive of activity is crucial, because it will transform our picture of the human blueprint from a static list of 3-billion DNA building blocks into the dynamic master-regulator that it is. Further research will be crucial in understanding how genes are controlled so that they leap into action at precisely the right time and place in our bodies. In addition, they will help explain how the carefully choreographed process can go awry, triggering birth defects, diseases and ageing.

The new analysis shows that more than 80% of the human genome is active in at least one biological process that the ENCODE team measured. Nearly all of it could turn out to be active when the data is more complete. Vast chunks of that activity is wrapped up with gene regulation which dictates whether the instructions each gene carries for making a unique protein will be executed or not. This regulation is key, because virtually every cell in the human body carries the entire set of 21,000 protein-making genes. To adopt its unique identity, each cell – be it one in the pancreas that makes insulin or one in the skin making pigment or hair – must activate only a subset of them. The switches flip when master-regulator proteins bind to them, or when chemical tags are attached to them by enzymes. Some of the switches have been right where scientists would have expected them to be, close to the genes they control. But many new ones have been discovered with some being extremely far away.

newphilo in reply to MarkDowe


Genomic statistical correlations are useful, but the testing and confirmation in the wet-lab require huge resources: PhD's, lots of money, and time. That is to say, do not expect useful results to soon.

newphilo in reply to newphilo

I was wrong assuming ENCODE data is the exclusive result of biostatistics.
As per,
"The maps were created using a variety of techniques, including chromatin immunoprecipitation (ChIP) to locate binding sites for 119 transcription factors and histones as well as chromatin conformation capture, methylation analysis assays, and RNAseq."


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