Field of Science

Down with the "Gene for X" nonsense already!

So how do I properly respond to a question like "Wouldn't putting fish genes in a tomato make it fish-like"?

I could go on explaining how genes don't actually carry any mysterious 'quality' of the organism they're found in, and generally just code for some protein that merely catalyses a specific chemical reaction. For example, jellyfish green fluorescent protein is just a fluorescent protein that gets most 'turned on' by blue light and changes it to green. It has nothing to do with jellyfish stings or tentacles or an aptitude for drifting behaviour. It was simply isolated from a jellyfish, and there's nothing fishy about it. Basically, GENETICS - UR DOIN IT WRONG. But in a more verbose and less condescending manner...

But then they respond that they don't believe you. That it just doesn't seem right. Ok, what do I do now? Not only have they got so much wrong I don't know where to begin fixing, they also have their faith, and information from someone who works with transgenic stuff on a daily basis is not going to be enough to change their minds.

First off, what the hell is the point of asking if you then don't 'believe' their response? If they had an argument of some sort against my story, or if they didn't understand some part, then by all means, ask away! But simply stating you don't 'believe' is a bit of a conversational cul-de-sac. Besides, it doesn't seem that genetics itself cares very much about what you believe.

Next, this leaves me wondering: where has public education gone wrong? How did the 'fish gene' concept emerge in the first place?

Perhaps this is an extrapolation of the "height gene" that permeates introductory genetics classes. Intro genetics is full of problems like "You cross a homozygous recessive short (tt) plant with a heterozygous tall plant (Tt)..." It seems that while convenient pedagogic tools for the study of heritability, problems like this distort the perception of how genes actually work. Genes do not code for qualities or traits - they are just A,T,C,G,N* strings that eventually make their way to being translated into amino acid language to become [hopefully] functional proteins. Playing around with this string of A,T,C,G can result in different phenotypes or physical appearances, starting from the shape and functionality of the protein and sometimes reaching all the way to physical appearance, such as height.

Seeing the gene as coding for a certain phenotype is messy and...well, wrong. Often one locus (gene) has several alleles (variants) which were found in screens for different things by different labs. For example, Arabidopsis rsw2 (radially swollen) was found along with rsw1 when screening for root swelling defects. This same locus was found by a lab studying the plant vascular system, and named irx2 (irregular xylem); dec (deffective cytokinesis) and acw (abnormal cell wall) by some other groups.

Does this gene code for forming a proper xylem, mediating proper cytokinesis or to prevent root swelling? Is this a 'Xylem Gene' or a 'Root Swelling Supressor'? What if I tell you defects in this gene result in substantial dwarfism? Is this yet another 'Gene for Height'? If you cross a short plant (homozygous rsw2) with a tall plant, your F1 progeny are all tall. Selfing the F1 results in 1:3 segregation of short:tall, respectively. Determine the genotypes...yadda yadda. See how useless and confusing this way of seeing genes can be?

The gene in question results in a protein chemically known as an 'endo-1,4-beta-D-glucanase' called KORRIGAN1 by biologists. It's believed to hang out near the cellulose synthase complex and cut the crystalising cellulose strands to relieve tension. (Reiter 2002 Curr Opin Plant Biol; pdf) All those mutants are results of point mutations and insertions in various parts of the same locus - many of the phenotypes actually overlap quite a bit, but the labs were focusing on different areas of plant biology, thus naming the allele as it was relevant to them. Yes, it can get quite messy!

Interestingly, different point mutations in this gene can have different phenotypes - implying there are several protein domains with different functions. Perhaps this thing acts in some sort of complex - the story is rather sophisticated at this point. But let's say it results in weakened cellulose fibrils due to crystalisation defects. Celluse is important in plant cell morphogenesis; essentially a plant cell expands like a balloon in a cage, with the cell wall acting like the cage in directing the expansion. Break the cage, and the balloon will tend to swell spherically. Thus the affected plant would end up with cell swelling. This disrupts growth in many tissues, eventually leading to problems with the vascular system and a severely dwarfed sick-looking plant. This gene doesn't 'code for' any of that, but defects thereof have far reaching consequences in the massive tangle of pathways that is life.

Of course, when you first find a gene, you don't know what it is yet, and thus name it after the mutant phenotype. This can lead to comical results - we have a 'Retinoblastoma-Related' gene in plants! No, plants haven't 'mutated/evolved eyes' (like 'evolve', 'mutate' should NEVER ever be used as a transitive is a strictly passive, non-volitional, non-directed event!) ... this gene is named after a homologous Retinoblastoma (RB) gene in the human system, where it may have been first isolated when studying the retinal cancer. While this gene does act in human eyes, this is not its 'purpose' or funtion it all. It carries no 'eye' qualities - its actual function is to supress DNA replication genes to prevent extra rounds of DNA copying out of turn. When it's broken, cell cycle problems follow, among them retinoblastoma in the human eye. Plants experience increased ploidy levels (number of copies of the genome) and hyperplasia in proliferating tissue. (reviewed in Inze & DeVeylder 2006 Annu Rev Genet; Gutierrez 2009 in The Arabidopsis Book) I hope it's clear by now that RB and RBR don't code for supressing retinoblastoma, but rather code for closely related proteins with very strictly defined chemical activities and precise functions affecting a multitude of pathways downstream.

Actually, the whole idea of genes having any function at all is an artefact of human reasoning (namely the intentional stance) - Dennett (1995 Darwin's Dangerous Idea) argues that while artefactual, the intentional is a powerful tool in inquiry as long as we acknowledge it doesn't actually imply a real 'purpose' encoded anywhere.

Population biologists (grrr) and evolutionary ecology folks ain't helping either. They intend to use the 'gene for blah' concept metaphorically, but that can easily mislead both the public and even some research in the field itself!

So if genes don't code for qualities or characters, how do you get from genes and proteins to organisms? We're working on that. The complexity of this problem will be enough to sustain many a developmental biologist with a lifetime of work (funding is whole other question altogether =( ) I intend to eventually share some snippets of the stories in that field... some of the mechanisms are truly elegant, others truly outrageous!

But hey, it works... otherwise you wouldn't be able to read any of this!

I do need to think up a simpler way of explaining 'how genes work'...

*Ah, the N, the phylogeneticist's worst nightmare and greatest blessing =P Freedom and ambiguity in one nice letter. (N stands for 'any' in FASTA format - ie A, C, T or G)
It's a bit creepy to watch phylogeneticists change 'edit' their sequences "Oh, that T shouldn't be there... *delete*" ...


  1. IANAgeneticist, but the last occasion on which I threw a book across a room was when I tried to read Dawkins' "Extended Phenotype" and faced the first chapter dedicated to justifying the "gene for X" usage.

    I may not know from genetics, but I can recognise specious logic when I see it.

  2. I think that there is probably no concept in science simultaneously trendier and more misunderstood than that of the gene.

  3. Oh, THAT'S why I got stuck at the beginning of The Extended Phenotype. I didn't really want to disagree with a world-famous evolutionary biologist back then, but there was something wrong. Then I fixed up my own ego ^_^ After having been thoroughly converted by the local protistologists to the Cult of Tom and constructive neutral evolution and the likes, I'm pretty much incapable of reading anything by mainstream evol biologists...

    Opisthokont - Two words: Quantum Physics.

  4. I really think the public NEEDS the word "allele" and to understand it. I notice that news media, like the New York Times, absolutely will not use the word! but I don't think genetics makes much sense when we use gene where we mean allele.


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