Junk DNA in the Toronto Star

 
Cameron Smith is an an environmentalist who lives Gananoque, Ontario (Canada). He was written more that 500 columns for the Toronto Star. Most of them are about nature. His latest column in today's Idea section caught my attention [Getting to the root of plant life].

The column seems to be heading in the direction of promoting the "intelligence" of plants (see below). There will be a followup column soon, according to Cameron Smith.

The part that disturbs me is the following,

However, with their mapping of the human genome, they [molecular biologists] discovered that humans carry only about 25,000 protein-coding genes. This was startling, because the simple nematode worm has about 19,000 such genes – and the human body is immeasurably more complex than a worm's. So, why didn't humans have a lot more protein-coding genes – genes that instruct proteins what to do?

I've addressed this point several times [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome, SCIENCE Questions: Why Do Humans Have So Few Genes?]. It's simply not true that all scientists were surprised by the number of genes we have. For many, this result was anticipated and it poses absolutely no problems in understanding biological complexity. There's no pressing need to look for some magic bullet.

To find answers, molecular biologists had to revise their notions of the genetic code. They knew that a huge number of genes in the human genome, making up more than 98 per cent of the genome, don't code protein. These they had previously dismissed as evolutionary leftovers, or junk DNA.

In an enormous turnaround, they began looking at these non-coding genes more closely and discovered they were not junk after all.

There's a lot of nonsense in those few sentences. The most important flaw is that the basic message is completely wrong. It is simply not true that molecular biologists have discarded the concept of junk DNA. The vast majority of molecular biologists know the facts; namely that >90% (probably more) of our genome consists of junk DNA. Just because there are a few renegade scientists who don't know any better does not make these facts disappear.

They had an extremely important function. A key to the mystery lay in the nature of complexity. There was no doubt protein-coding DNA was capable of creating complexity.

It could issue instructions for creating the legions of proteins that, in the case of humans, make up half their dry weight. But regulating the process was another matter. Without regulation, the results would be mostly chaotic.

In addition, as the complexity of organisms increased, the amount of regulation that was needed increased exponentially.

Regulation, it turns out, is the job of RNA (ribonucleic acid), located in the nucleus of cells along with DNA. It's from the so-called junk DNA that RNA gets regulatory instructions.

This revelation opened the intellectual floodgates, and put to rest the notion that life was ruled by a robotic DNA ritually coding proteins, much like a machine stamping out widgets.

Here are the scientific facts in a nutshell.

• Scientists have known about regulatory sequences for at least fifty years. They were never, ever, thought to be junk DNA by any competent molecular biologist.
• There is no evidence to support the half-baked notion that the amount of DNA sequence required for regulation of "complex" organisms (i.e., humans) is exponentially more than that required for regulation of "simple" organisms (i.e., nematodes). All available evidence shows that gene regulation in all multicellular species is very similar.
• We've known about regulation by small RNA's since the 1970's. Nothing new there. There is no solid evidence to suggest that regulation of typical human genes requires RNA and much theoretical and experimental evidence against such an idea. Active imagination doesn't count in science. Scientists need real data before jumping to the extraordinary conclusion that human gene regulation is fundamentally different than other species.
• One of the many reasons for accepting that only 2% of our genome is functional has to do with the concept of genetic load [Facts and Myths ...]. If junk DNA is full of genes encoding regulatory RNAs then we're in big trouble because mutation rates are going to kill us off pretty quickly.

Cameron Smith seems to be quite taken with the ideas of Anthony Trewavas at the Institute of Molecular Plant Science, University of Edinburgh (Edinburgh, UK). Trewavas has been writing papers promoting the idea that plants have a form of intelligence. He doesn't mean they have a brain, of course, what he means is that plants have a complex form of regulation that responds to the environment.

According to Trewavas, systems biology and computer modeling have revealed a level of complexity that scientists never suspected (Trewavas, 2006). Naturally, this totally unsuspected level of regulatory complexity has been hidden from those scientists who have adopted a reductionist approach to science.

Systems approaches enable plant scientists to understand the structural stability of plants, their control and design structure, and how these lead to robust and resilient behavior. These capabilities are the result of a complex biological system in which control operates at many different levels (Figure 1). Complexity is a serious biological problem, and it is likely that biological systems are the most complex known. Increasingly, scientists are going to have to depend on computational biologists to construct models that can then be tested back in laboratory conditions. However, as indicated here, laboratory conditions are only one environmental circumstance among many in which plant systems develop. In 10 years, my own estimate is that plant molecular research groups will be half modelers and half wet investigators producing new data for modelers.

I'm getting a little tired of this sort of rhetoric. Systems biology, properly defined, can be a very useful approach to a problem but turning it into a religion isn't going to help. I'm content to wait and see whether the systems biologists are actually going to deliver something (other than rhetoric) before jumping on that bandwagon.

Trewavas believes in the power of information theory (IT). This faith him to conclude that plants have a form of intellignece (Trewavas, 2005a, 2005b, 2003).

This idea of intelligent plants should not be taken literally. Trewavas clearly means it to be controversial and clearly understands that it is a metaphor. However, the concept is based on an false premise, in my opinion. The premise is that there is a complex sophisticated (and largely undiscovered) regulatory circuit in plants that allows them to behave as though they were responding to the environment in an intelligent way. I don't think we need to go down that path. Yes, plants can control gene expression, just like bacteria, but I see no value in exaggerating that control to the extent that Trewavas does.

From the current rate of progress, it looks as though plant communication is likely to be as complex as that within the brain. (Trewavas, 2003, p.6).

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Trewavas, A. (2003) Aspects of plant intelligence. Ann Bot (Lond). 92:1-20. [PubMed]

Trewavas, A. (2005a) Plant intelligence. Naturwissenschaften. 92:401-13. [PubMed]

Trewavas, A. (2005b) Green plants as intelligent organisms. Trends Plant Sci. 10:413-9. [PubMed]

Trewavas, A. (2006) A brief history of systems biology. "Every object that biology studies is a system of systems." Francois Jacob (1974). Plant Cell. 18:2420-2430. [PubMed]