Are you familiar with the facts of sexual reproduction (the sort that has evolved the most complex systems)? Take a wonderfully fit organism, whose systems are wonderfully integrated, and who will go on to reproduce with wonderfully fecundity. It will do so by means of gametes (sperm or ova). To produce a gamete, chromosomes that came from the organisms father are paired up with the ones of corresponding structure. Each pair of chromosomes is lined up, sliced at many random locations into pairs of strips, and a a new chromosome is assembled by taking a paternal strip or a maternal strip at random. That will then be combined with a similarly produced gamete from a mate.

Therefore you can rave all you like about the integration of biological systems and the wonderfully holistic way they function and it’s all perfectly irrelevant. The integration is rudely thrown away and all that’s used of a fit organism is half its genes.

CK: “Not to mention, you still didn’t even come *close* to addressing the fact that not all information that is heritable (even at a molecular level), is found in genes (think epigenome).”

I’m remiss for not addressing that, but the answer is simple: it doesn’t change anything. DNA genes will have to be “selfish” on average against the pseudo-random background of non-DNA inheritance, the same way they already have to be “selfish” against the pseudo-random background of other DNA genes. Moreover to the extent the non-DNA mechanism has atoms of inheritance analogous to DNA genes, they will have to be “selfish” as well.

“But gene x is the more helpful thing to focus on, because it’s the thing that endures and is causal with respect to the next generation.”

Is *not* more helpful…..because you don’t understand what gene x will do unless you understand the system it is being introduced in. The system determines what gene x will do, not gene x. And no, gene’s aren’t persistent (they die quite easily and rapidly, sometimes within one generation span), but system properties *are* persistent. Genes last for as long as the systems can tolerate them. Then either they or the system they exist in vanishes as well.

You still continue to pick and choose what you will address, ignore that which contradicts what you say, and continue to talk in vague terms about a subject in which it increasingly appears that you are fairly unfamiliar. I’m leaving off here because I really think it is useless to argue the point. Actually get in a lab and do some genetics work.

Nonsense. Systems get _tested_, but they don’t get _selected_, they get torn down for scrap and (in the common case of sexually reproducing organisms) are never replicated exactly again except by wildly improbable and unimportant accident. It’s the genes that built the systems that get selected – they pass on as exact copies into the next generation.

CK: “Systems, simply put, are components that are integrated in some manner to have specific properties – this is really important since individual genes *don’t* do anything…systems do. ”

Again, nonsense. No biological system is ever literally integrated. Biological systems are thrown together literally at random from genes that have produced complex systems with useful properties in the past (plus a few mutations) and the result is either a complex system with a useful property or it isn’t.

CK: “[...] If system B is selected for, it’s because of the properties of the new system…*not* because of the new gene introduced.”

These are not contradictory. Indeed since, ex hypothesi, system B is produced by introducing gene x, they’re exactly the same thing. But gene x is the more helpful thing to focus on, because it’s the thing that endures and is causal with respect to the next generation.

http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=10470

Whether you like it or not Mark, such a narrow, reductionist view of biology, such as the one you would like to espouse and champion (along with Dawkins), is dieing out and being replaced by a much more comprehensive and understandable approach.

“At any particular time for any particular species there is some fact of the matter about the average effect of a gene, which is a function of the environment and the other genes in the genepool.”

But what you don’t realize is that individual genes do *not* get selected for…systems do. Systems, simply put, are components that are integrated in some manner to have specific properties – this is really important since individual genes *don’t* do anything…systems do. So this could be a biological pathway in which the gene is the component, or a regulatory network in which biological pathways are the component, or one individual of a species and all its regulatory networks are one component, etc., etc., etc. For instance, take System A that provides some function (doesn’t matter good, bad, whatever, it just does *something*). Add gene x to System A, and it becomes System B (not System A + gene x): this is important because by adding something to the system, you actually modify the entire system to some degree, literally making it a different system, albeit with similar properties. If system B is selected for, it’s because of the properties of the new system…*not* because of the new gene introduced. You could potentially make modifications to the old System ‘A’ that would give it the same properties as System ‘B’, without introducing any new genes, and you could get the same effect. To make this metaphor even more poignant take two points about biology:

1. Not all information that spells out what an organism will do is inherited in its genes. The epigenome (methylation patterns across the genome), also encode a tremendous amount of information that determine how the system will work.

2. At some point, genes didn’t exist. What then was the fundamental unit of selection?

Your dogged insistence that selection only exists (or is only relevant) at the gene level is moot, and such a dogmatic view isn’t considered to being close to *fact* in the realm of biology (at least as far as *facts* are determined as such in the realm of science). So, to state that such is the case, and use that as a jumping point to show why, as you stated earlier:

“…evolution doesn’t optimize for the good of the species, it optimizes (or at least pseudo-optimizes) for the good of individual genes. Sometimes this lines up with the good of the individual, or the species, and sometimes it doesn’t.”

as a way to argue against how ideas of selection could even be applicable outside the realm of DNA (such as cultural ideas and institutions) is absurd.

I read the article and I’m not seeing an argument. It’s completely irrelevant how complex and multivalent a gene is, or how many other genes it has to interact with to be expressed. At any particular time for any particular species there is some fact of the matter about the average effect of a gene, which is a function of the environment and the other genes in the genepool. If the average effect of a gene does not have the result of causing a break-even or better number of copies of that gene in the next generation, then it simply cannot persist, no matter how good those same effects may be for the species as a whole.

http://www.greythumb.org/blog/index.php?/archives/17-Evolvability-Suppression-to-Stabilize-Far-Sighted-Adaptations.html

http://www.guardian.co.uk/education/2005/may/06/science.highereducation

Again, to tired to read through the whole post – plus this goes more into the cool aspects of systems biology than the blog, and shows how this view of the biology is literally remapping the course of evolution in a whole new way.

http://www.arn.org/blogs/index.php/2/2005/05/10/no_more_selfish_gene_biology

Systems biology is reasserting its primacy in understanding the evolution of species, and even entire ecosystems…whether you or Dawkin’s would like to admit it, his theories are just that – theories. They may have been understandable, and even allowable in a naive sort of way, but it fails on all accounts to actual provide testable hypothesis to further our understanding of biology and its underlying natural selective forces. Now that it is possible to sample entire transcriptomes, and look at how whole systems react to small perturbations, such a simplistic viewpoint is simply naive. I only post this here because I ran across while look at more systems biology stuff – which is the main field of focus in my graduate degree. Hopefully it will be of use to someone else out there looking into the fascinating field of systems biology – and is tired of Dawkin’s myopic view of the wonder that is life.

Peace