May 6, 2005
MORE THINGS IN HEAVEN AND EARTH
The unselfish gene (Johnjoe McFadden, The Guardian, May 6th, 2005)
But a gene without function isn't really a gene at all. By definition, a "gene" has to make a difference; otherwise it is invisible to natural selection. Genes are those units of heredity that wrinkled Mendel's peas and are responsible for making your eyes blue, green or brown. A century of reductionist biology has tracked them down, through Watson and Crick's double helix, to the billions of A, T, G and C gene letters that were spewed out of the DNA sequencers. But now it seems that the genes, at the level of DNA, are not the same as genes at the level of function.The answer to these riddles is being unravelled in an entirely new way of doing biology: systems biology. Let's return to that road network. We may identify a particular road, say the A45, that takes goods from Birmingham to Coventry, and call it the BtoC road, or BtoC gene. Blocking the A45 might be expected to prevent goods from Birmingham reaching Coventry. But of course it doesn't. because there are lots of other ways for the goods to get through. In truth the "road" (or gene) from BtoC isn't just the A45 but includes all those other routes.
Rather than having a single major function, most genes, like roads, probably play a small part in lots of tasks within the cell. By dissecting biology into its genetic atoms, reductionism failed to account for these multitasking genes. So the starting point for systems biologists isn't the gene but rather a mathematical model of the entire cell. Instead of focusing on key control points, systems biologists look at the system properties of the entire network. In this new vision of biology, genes aren't discrete nuggets of genetic information but more diffuse entities whose functional reality may be spread across hundreds of interacting DNA segments.
This radical new gene concept has major implications for the gene hunters. Despite decades of research few genes have been found that play anything more than a minor role in complex traits like heart disease, autism, schizophrenia or intelligence. The reason may be that such genes simply don't exist. Rather than being "caused" by single genes these traits may represent a network perturbation generated by small, almost imperceptible, changes in lots of genes.
And what about "selfish genes", the concept introduced by the Oxford biologist Richard Dawkins to describe how some genes promote their own proliferation, even at the expense of the host organism? The concept has been hugely influential but has tended to promote a reductionist gene-centric view of biology. This viewpoint has been fiercely criticised by many biologists, such as the late Stephen Jay Gould, who argued that the unit of biology is the individual not her genes. Systems biology is reasserting the primacy of the whole organism - the system - rather than the selfish behaviour of any of its components.
Systems biology courses are infiltrating curricula in campuses across the globe and systems biology centres are popping up in cities from London to Seattle. The British biological research funding body, the BBSRC, has just announced the creation of three systems biology centres in the UK. These centres are very different from traditional biology departments as they tend to be staffed by physicists, mathematicians and engineers, alongside biologists. Rather like the systems they study, systems biology centres are designed to promote interactivity and networking.
And of course, outside of biology, there will be many who will be saying, "I told you so". Holistic approaches have always dominated the humanities and social sciences. The first eight chapters of Salman Rushdie's Midnight's Children describes the lives of the narrator's grandparents, parents, aunts, uncles and friends against the backdrop of the tumultuous politics of 20th-century India and Pakistan. The reason, according to the narrator, is that "to understand just one life, you have to swallow the world". Perhaps biologists ought to have read more.
We will miss all those just so stories.
One does though admire the honesty with which they reduce their putative science to a comparison with a magical-realist novel.
Posted by: oj at May 6, 2005 9:17 AMWhen the human genome was published the most striking feature of human DNA was how *few* genes we really had. And of those genes, only 100 were different than those of a lab mouse (whose genome was published at the same time).
When researchers began unraveling DNA they anticipated tens of thousands of genes to account for the complexity of the human mind and body. They assumed that they could find the gene for mathematical prowess, musical genius, or even high jumping ability. What they found is that the genes are merely the first in a complicated chain of events which create a human.
Its the *proteins* created by the genes and the subsequent multiple interactions of these proteins with each other (and the proteins that they make, and the proteins made after that, and so on) which creates a person. The whole process is complicated to the point of invoking chaos theory, in that the processes may be deterministic but untraceable and unpredictable. Each gene is apparently wholly or partially responsible for multiple physical and mental characteristics. Disturbing one gene may result in a daisy chain of unforeseeable results. So even if they found the genes for blond hair and blue eyes, altering them may also result in an idiot savant, albino with webbed toes (e.g.).
If (as it seems likely) the multiple level gene and protein productions/interactions which make a human being are complex to the point of being classified as "chaotic", then we can no more understand or trace these interactions than we can travel faster than light. There is no "gene" for height, or musical ability, or blue eyes, or male pattern baldness (much to my chagrin). These things are the result of probably nontraceable (chaotic) interactions between proteins made by genes and the other chemical made by proteins, and their interactions, etc.
daniel duffy:
I was shocked to read an article a few years ago which went over issues of the genome and brain chemistry in detail and included the observation that some scientists feel tempted to throw up their hands and conclude that this subject may simply be too complicated for the human mind to figure out -- in the same manner, I suppose, as the human world is too complicated for a dog to understand.
Not sure if that's true or not, but to hear something like that from scientists is amazing and gives ample voice to their frustration over this subject.
Posted by: Matt Murphy at May 6, 2005 6:03 PMSee Wallace Arthur, "Theories of Biology," written in 1987, for a full discussion of the appropriate weight to be given to the physical/mathematical approach to genetics.
It is a fantasy of ignoramuses like daniel that researchers expected to find a gene for math.
I really don't get you other guys. The discoveries of biology are not a secret. You could look them up.
But you don't and you expose yourselves, over and over, as know-nothings. I understand why Orrin does it. But the rest, it's a puzzlement.
That the Guardian is a whole generation behind on biology is not particularly a surprise.
Posted by: Harry Eagar at May 6, 2005 8:05 PMharry, its easy to call names and pretend to know more than everyone else, but at the end of the day you are just parroting what you have read, too. you haven't discovered or invented anything, either. how different are the speculative theories of this or that biological "expert" from the chin music coming from people like hawkings ? i think everyone here is after the same things: insight, knowledge, truth, and some spirited discussion.
so many areas of research are politicized now that it is not possible to grant any researcher the benefit of the doubt.
now i am a s/w engineer and its pretty clear to me that dna is analagous to a computer program. figure out the language and its rules, and all will become clear. biologists are analagous to h/w engineers, so most likely the true break throughs won't come from them.
how about sharing some of your obvious knowledge on the subject, and be a better person than harry reid ?
Posted by: cjm at May 6, 2005 11:34 PMWell, it does not surprise me that people who invent gods also think they can invent biologists. The difference being that there is no real god to check your fantasies against, while there really are biologists.
Before we get to the insight stage, it might be as well to check and see what the real biologists did say, instead of -- as daniel does -- just making crap up.
You want me to share. I already directed you to the excellent Wallace Arthur, one of the clearest thinkers in biology. (Unfortunately, I misremembered the title of the book. It's 'Theories of Life.' Been 20 years, which is how far you guys are out of date.)
Want more? OK. On the pattern of causal interconnections underlying development (what daniel wants to be talking about): 'Morphogenetic complexity depends on the activation/inactivation of gene sets, not single genes . . . '
That's from J.H. Sang in 'Genetics and Development' written back in 1984.
It is not possible to conduct a seminar on a subject as complex as biology on a blog, even if I were qualified. You have to go out and actually devote some effort to becoming informed.
Here's another 'insight,' one I just learned about yesterday: You have a gene, named SCML, in you that codes for the sex comb on the midleg.
I bet you have neither sex combs nor middle legs, but you do share genes with fruit flies.
Since you are a software engineer, I recommend Arthur's chapter 9, 'The Variable Gene Activity Theory of Cell Differentiation' and chapter 10, 'The Missing Theory of Development.'
You might change your views about how closely DNA compares with a computer program.
Posted by: Harry Eagar at May 7, 2005 1:18 PM
It is no surprise that people who imagine they can create gods would also think they can create biologists.
The difference is that while there is no god to check your fantasies against, there really are biologists and we can look in books to see what they said, instead of just making crap up, like daniel.
Let's look in J.H. Sang's 'Genetics and Development.'
Writing about patterns of causal interconnections underlying development (what daniel incorrectly imagines he was writing about), Sang says, ' Morphogenetic complexity depends on the activation/inactivation of gene sets, not single genes . . . ' That was published in 1984.
It is beyond either my competence or the parameters of a blog to run a seminar on biology, but I did try to direct you to Wallace Arthur, one of the clearest thinkers in biology. (Unfortunately, I misremembered the title. It's 'Theories of Life.' Been a while since I'd read it.)
It is not a pretense that I know more about what biologists say than others here (I won't say all others, but you know who you are). Once we all were on the same page about what biologists say, then we could go on to debate what insights we might have about that.
Let me suggest that the approach of making crap up will not lead to any considerable insights.
As for your comparison of DNA to software, it may be a lot more complicated than that. I recommend Arthur's chapter 9, 'The Variable Gene Activity Theory of Cell Differentiation' and chapter 10, 'The Missing Theory of Development' to you.
Posted by: Harry Eagar at May 7, 2005 2:17 PMHmmm. Sorry about that. My first post was not showing, so I repeated myself.
Posted by: Harry Eagar at May 7, 2005 2:19 PMhmmm, apologies for double posting but nothing for all the name calling; ok. i may not know as much as you do about biology (but more than you think i know) but i do know that the refresh control on a browser will help avoid double posting.
there are, what, 8 or so amino acids used to describe all dna sequences ? [i didn't look up the exact number because i wanted you to be able to correct me] that is a language; all statements (genes) are produced from this small set of elements. proteins are the output of the program.
i await your courteous and informative reply, or is this going to be another case of "its too complicated to explain here" ?
Posted by: cjm at May 7, 2005 3:46 PMThere aren't any amino acids in DNA, so, yes, it might take more space than a blog post to explain it to you.
I don't believe that you know more biology than I think you know, and I don't think you know any.
But I can try to explain why you have oversimplified. The DNA-protein system is not like a slot machine at Vegas -- put in a nickel and get lots of nickels back.
To take a very simple case, during development of a sheet of tissue, which needs to differentiate into different kinds of cells, chemical signals (proteins, enzymes) feed back to a control gene that acts something like a rheostat. Depending on the concentration of this enzyme, this gene produces (more precisely, directs the production of) another protein that switches on or off another gene that produces a different signal chemical that switches on or off yet a different gene that produces (or shuts off) a protein that, when it reaches a threshold concentration in the growing cells of the tissue causes the cells to differentiate.
Although it's beyond my competence, some of these systems (not all) have now been described down to the level of action of individual atoms.
You seem to imagine that DNA is a code (which is correct) that, given the key, reads off proteins (also correct). There is more to it than that.
Interestingly, in the earliest stages of development, the genes are not switched on at all. The initial signals (up to blastomere stage, at least in Drosophila) come from proteins inherited from the mother and packaged along with the nucleic acid of the new individual in the surrounding cytoplasm of the egg.
Posted by: Harry Eagar at May 7, 2005 10:07 PMThere aren't any amino acids in DNA, so, yes, it might take more space than a blog post to explain it to you.
I don't believe that you know more biology than I think you know, and I don't think you know any.
But I can try to explain why you have oversimplified. The DNA-protein system is not like a slot machine at Vegas -- put in a nickel and get lots of nickels back.
To take a very simple case, during development of a sheet of tissue, which needs to differentiate into different kinds of cells, chemical signals (proteins, enzymes) feed back to a control gene that acts something like a rheostat. Depending on the concentration of this enzyme, this gene produces (more precisely, directs the production of) another protein that switches on or off another gene that produces a different signal chemical that switches on or off yet a different gene that produces (or shuts off) a protein that, when it reaches a threshold concentration in the growing cells of the tissue causes the cells to differentiate.
Although it's beyond my competence, some of these systems (not all) have now been described down to the level of action of individual atoms.
You seem to imagine that DNA is a code (which is correct) that, given the key, reads off proteins (also correct). There is more to it than that.
Interestingly, in the earliest stages of development, the genes are not switched on at all. The initial signals (up to blastomere stage, at least in Drosophila) come from proteins inherited from the mother and packaged along with the nucleic acid of the new individual in the surrounding cytoplasm of the egg.
Posted by: Harry Eagar at May 7, 2005 10:11 PM