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Tuesday, June 14, 2022

Distrust simplicity (and turn off your irony meters)

I just stumbled upon an opinion piece published in EMBO Reports on May 22, 2022. The author is Frank Gannon who is identified as the former Director of the QIMR Berghofer Medical Research Institute in Brisbane, Australia and the title of the article is "Seek simplicity and distrust it."

I'm about to quote some excerpts from the article but before doing so I need to warn you to run off your irony meters—even if you have the latest version with the most recent software updates.

Gannon's main point is that scientists should seek simple explanations but they must be willing to abandon them when better data comes along. He gives us some examples.

However, it seems that there is a collective amnesia among scientists such that we forget to distrust the simplicity that we pursue on our path to insight. The central dogma of molecular biology—that information flows unidirectionally from DNA to RNA to protein—was overturned, at least in part, with the discovery that this linear cascade could be reversed by reverse transcription.

Really? The Central Dogma of Molecular Biology was overturned, "at least in part," by reverse transcriptase? (It wasn't.) If you are going to write about a topic like this then you'd better make sure you know what you're talking about.

The great quote from Jacques Monod “What is true for E. coli is true for the elephant”, held valid only until the discovery of introns in eukaryotes. As I was close to the earliest data that pointed to the existence of split genes, I am well aware of the incredulity of biologists when they realised that genetic material did not have the same simple design irrespective of the organism.

Monod's statement was never supposed to be taken as literally as that.1 He was referring to the unity of biochemistry (Friedman, 2004). This is clear from what he says in Chance and Necessity, "Today we know that from the bacterium to man the chemical machinery is essentially the same, in both its structure and functioning." He meant that all species have DNA, RNA, and protein and that these molecules carry out the same roles in humans as they do in bacteria. The essence of this simple observation is as true today as it was 50 years ago.

The death of “Junk DNA”—a term, coined in 1972 by Susumu Ohno for the non-coding parts of the genome—has been more gradual. The perception that exons are the only useful part of the genome has been proven wrong with the discoveries of noncoding RNA, the controlling roles of intra-genomic areas, the essential interactions between distant genomic regions and peptides encoded by short open frame regions.

Did you turn off your irony meter? Don't say I didn't warn you. Jacques Monod (and Susumu Ohno) would be surprised to learn that in 1972 they knew nothing about noncoding genes and regulatory sequences.

More seriously, how did we ever get to the stage where a prominent scientist who frequently publishes opinion pieces in EMBO Reports could be so ignorant of the junk DNA controversy after all that's been written about it in the past ten years?

1. Besides, introns exist in bacteria.

Friedman, H.C. (2004) From Butyribacterium to E. coli: An Essay on Unity in Biochemistry. Perspectives in Biology and Medicine 47:47-66. [doi: 10.1353/pbm.2004.0007]


William Martin said...

The Friedman essay is very worthwhile. The story of "too much function" is the story of too much politics. Imagine all the function some of those big genomes have in store, 44 times more function in lungfish genomes. Or Japanese canopy plant, 50 times more function. Wow. But, let people believe what they want to believe. I can't remember who, if anybody, said that "exons are the only useful part of the genome."

Anonymous said...

Irony indeed. In an article arguing against using simplistic explanations we find the use of simplistic, and often wrong, portrayals of molecular biology.

Piotr Gąsiorowski said...

Aren't the eukaryotic mechanisms of intron excision partly shared with Archaea and inherited from them?

John Harshman said...

Is the inability to sign in and escape the "Anonymous" label limited to Safari? Chrome seems unaffected. How can those using Safari fix this problem?

Arek Wittbrodt said...

No. I have the same problem on Firefox. On Chrome everything seems ok.

Don Cates said...

Firefox comment using 'Name/url'

Don Cates said...

Firefox comment using 'Google account'

John Harshman said...

Odd. On Safari, "Google account" isn't working.

John Harshman said...

But it does work on Firefox

Donald Forsdyke said...

My two bicyclists friends function equally well. Up hill, down dale, they go neck to neck. It is quite surprising, since one carries 50 spare tyres in his backpack, whereas the other has a small puncture repair kit. It seems the terrain they cross is particularly prone to generate punctured tyres and it is quicker to simply replace with a new tyre than repair with the kit. Nevertheless, the heavy backpack is a disadvantage when climbing hills. It seems the advantages and disadvantages cancel out.

John Harshman said...

Let me help you with your analogy. Instead of lots of spare tires, your friend carries millions of random scraps of rubber, a few of which can occasionally be used to patch a tire. Fortunately, these scraps, despite their great bulk, weigh almost nothing, so they don't slow him down significantly.

Escaping the analogy, junk DNA is, by and large, useless, and does not function to any real degree as a collection of spare tires. But apparently it takes little enough energy to copy that there is no selection against it.

Paul Hamel said...

Just a small point. As I understand it, The Central Dogma pertained to the flow of information and then once encoded by (translated into) protein, that information could not be retrieved genetically (that is, back "upstream" into RNA and DNA). As stated "Once information has got into a protein it can't get out again" The model did, in fact, predict the transferage of information from RNA to DNA as a possibility.