Tuesday, February 13, 2007

Organisms, Groups, and Memes: Vehicles or Replicators? Part 1

An active replicator is that which exerts at least some kind of influence over the likelihood of its being copied. A DNA molecule is a replicator; a piece of sheet music considered valuable enough to be xeroxed can be considered a replicator (Dawkins, p. 83); but an individual organism, sexual or asexual, cannot be considered a replicator.

Here's why.

Because we reject Lamarckism, we know that characteristics acquired during an organism's life cannot be passed down to its offspring. Even in the case of asexual reproduction in which the entire genome is passed down, any acquired features--a lost limb, developmental factors, etc.--is not replicated in the lineage, and in order for the organism as a whole to be called a replicator it must pass these on. "There is a causal arrow," writes Dawkins, "going from gene to bird, but none in the reverse direction." However, the genome of an organism that reproduces asexually could be a candidate for the term "replicator."

Can a species be considered a replicator? Again, Dawkins points out that a species, being mutable, is not comparable to a gene and its alleles. However, the gene pool of a reproductively isolated species could be a candidate.

In examining this possibility, Dawkins explores "differential lineage extinction"--for example, the statistical rates of extinction of ammonites and bivalves that have a high rate of evolving a larger size, say, than those who do not (those that more rapidly increase their size over successive generations are also more likely to die off). However, while these different rates of extinction are a form of selection, they do not drive "progressive evolutionary change" and thus these lineages are not replicators, either. They are merely, as Dawkins terms them, "survivors."

(And at this point, people, I confess I must read the chapter again.)

Part II: Punctuated Equilibrium and Memes

48 comments:

Lui said...

I too must read the chapter again, as I've always been rather mystified by species selection, and quite frankly, the whole concept annoys me a bit. I think Dawkins has no problem with a limited form of it, though, it's just that, in his words, "it doesn't seem to do very much". On this I agree with him, and the reason is fairly obvious: for a complex adaptation to be built up, you need a steady generational replacement cycle. Organismic generation time far outpaces lineage duration, which can take millenia. Even with the advent of a new species, the trait could go in either direction. The organismic generational replacement cycle leaves it completely for dead, and will therefore swamp it.
"Differential lineage extinction" might be able to affect some simple, very general changes, like an average elongation in leg length, but nothing like the complexity of the human brain.
In The Ancestor's Tale, Dawkins talks about "clade selection", and how the "evolution of evolvability" might lead to certain lineages being selected over others because they are good at evolving (perhaps members of the lineage have more limbs which can be specialised, or some other such feature that is conducive to innovation and can allow the lineage to give rise to more offspring lineages than it otherwise would be able to, as those offspring can fill more ecological niches). It could also be because of the dispersion capabilities of a lineage that allow it to give rise to more offspring lineages.
I have a vague sense for why the gene pool of a reproductively isolated lineage might be regarded as a replicator, but I’m not so sure about why the lineage itself is not. I suspect it might go something like the following: the gene pool can be seen as a copy of the parent population but with a “mutation”, which might be the result of its being only a small statistical sample of the entire genetic variability of the parent population (even if the sample is a good one, the local conditions will drive the gene pools progressively further apart, provided that the isolation if maintained). It is within a gene-pool that Darwinian natural selection occurs, and it thus undergoes positive evolution due to local allele replacement. The conditions under which an isolated population finds itself, on the other hand, are largely the result of chance. Species don’t strive towards cladogenesis, it just happens for arbitrary reasons.

I have been thinking about this sort of thing for a while now, contemplating the nature of Homo sapiens. Obviously the human brain is the result of natural selection, just as much as the eye is, or any other complex organ, but that wasn’t my concern. I was thinking of the contingencies that brought about the conditions under which intelligence could evolve to the degree it has in our lineage. In retrospect, what would it take to evolve human like intelligence? Is it possible that sequence of conditions under which our lineage had to survive is the only one, or one of few, that a species with intelligence would have had to go through in order to do this? This sequence could be exceedingly unlikely, and that might be the reason why we are the only such species. You could apply a similar rationale to any adaptation: echolocation, electrical detection of prey, flight, etc. Some will be “easier” to arrive at than others, and there are plenty of examples of convergent evolution, where distantly related species “reinvent” the same sorts of solutions to similar problems. I think it was Stephen Gould who remarked once, “The human race was a happy accident”. He of course didn’t mean that we came about “by chance”, in the sense that creationists love to crap on about; I think what he must have meant was that the contingencies that our ancestors found themselves living under were essentially random (you know more Gould than I do, so correct me if I’m wrong), even while within population natural selection was going on to respond to those conditions. Tying this back to what I was saying about above, the probability that any particular lineage will hit upon human-like intelligence may be exceedingly small, but the odds that some lineage may eventually hit upon it may be quite good, given the millions and millions of years, and the millions of lineages that evolution has at its disposal.

If chance events like these were to cease, we might only have arms races and coevolution to keep us occupied! Anagenesis would continue on, but cladogenesis could stop altogether (though I'd have to look more carefully at sympatric speciation to say this with any confidence).

dogscratcher said...

"Because we reject Lamarckism, we know that characteristics acquired during an organism's life cannot be passed down to its offspring."

Can this definition accomodate symbiogenesis?

Kristine said...

Sorry that I haven't gotten back to you guys--I had a busy day at work and I had class on Valentine's Day night!

Indexing class. Ewww. Gimme an hour on the bus to get home, and I shall answer. :)

Kristine said...

for a complex adaptation to be built up, you need a steady generational replacement cycle

Exactly so. And I think Dawkins demonstrates this ably. I think his analogy was the evolution of the whale and the complex interrelationship that would accomplish this--hardly the stuff of species-level selection.

I get the idea that the concept of species selection annoys him as well, but that he includes it for the sake of fairness, because it seems to be theoretically possible (and I must say, Dawkins is one of the most scrupulously fair and even-handed writers that I have come across).

I think your characterization of Gould is correct. However, Gould had a thing about evolution not being progressive (or perhaps that's not the word to use). I always took issue with this. The essense of Gould's view was that the individual is the unit of selection, and that is what I took from his writings; it has created a great barrier for me in understanding Dawkins' view, but Dawkins keeps referring to the Necker cube as an analogy for how one can toggle between the concept of the individual and the concept of the individual's genome. I struggle with this, too.

I need to read what you've said about lineages more carefully because once again I feel that I'm in over my head.

Can this definition accomodate symbiogenesis?
I'm not sure that I understand the question. Are you asking if symbiogenesis is a form of Lamarckism? I don't have an answer for you--I don't know enough about the concept of symbiogenesis. (This isn't why Lynn Margulis came up with, is it?) I'll look it up.
:)

dogscratcher said...

"Are you asking if symbiogenesis is a form of Lamarckism?"

It seems to me it is a kind of Lamarkism, though a very limited version.

I just think, with symbiogenesis in mind, that the statement, "we know that characteristics acquired during an organism's life cannot be passed down to its offspring," is too strong.

Lui said...

Hi Kristine, I think I get it now! I've read the chapter again and I think I really do have a somewhat clearer understanding about what he's going on about. I wrote my original message before I even started re-reading the chapter, and some of what I said was just my attempt at a guess as to what Dawkins must have meant by a gene pool being a replicator. I can see that I was in error to automatically assume that a daughter species could be seen as a "copy" of the parent species, because I didn't take into account the apparent prerequisite of a homeostatically buffered gene pool. For them to qualify as replicators, they need to exhibit the features of homeostatic buffering and reproductive isolation. They might pass through the sieve of selection and survive (hence "survivors"), but that does not make them proper replicators. Let's go into that now.

Dawkins has this to say: "The best case I can make for regarding species, or rather their gene-pools, as multiplying replicators arises from the theory of 'species selection' associated with the palaeontological idea of 'punctuated equilbiria'." (p101. He later goes on to talk more about PE and how it might be related to the game theoretic ESS. He also mentions that perhaps Gould and Eldredge fail to give proper recognition to the possibilities offered by arms races)

He later writes: "For simplicity I have discussed the theory of species selection as one in which the species is treated as a replicator. The reader will have notice that, however, that this is rather like speaking of an asexually reproducing organism as a replicator. Earlier in this chapter, we saw that the test of mutilation forces us strictly to limit the title of replicator to the genome of, say, a stick insect, not the stick insect itself. Similarly, in the species selection model, it is not the species that is the replicator but the gene-pool. It is tempting, now, to say, 'In that case, why not go the whole hog and regard the gene as replicator rather than some larger unit, even in the Eldredge/Gould model?' The answer is that if they are right about a gene-pool being a coadapted unit, homeostatically buffered against change, it might have the same kind of right to be treated as a single replicator as has the genome of a stick insect." (p108)

So, why is it important that the population be homeostatically buffered (self-restoring to some stable set when a change occurs)? In case you found the above a little cryptic, I'll reword it: in the same way that the entire genome of an asexual organism might be regarded as a replicator (even as a single "gene") a gene pool must exhibit something similar, the property of constancy. We know that the genome of a sexually reproducing organism is emphatically not a replicator because it is fragmented by the effects of meiosis, and is not constant enough to reserve the status of replciator (Bits and pieces of the genome are properly regarded as replicators, of course). In the same way, the gene pool of a species that is not homeostatically buffered against change is obviously changing too often to be regarded a single, coherent entity, and is therefore not a replicator.

Continuing on: "The gene-pool has this right, however, only if it is reproductively isolated, just as the genome has that right only if it is reproduced asexually. Even then the right is a tenuous one."

It is because certain genomes are asexual that they can be regarded as replicators - they mixed their contents with other genomes, they would by definition not be asexual any more and could not therefore qualify as replicators. In the same way, a gene pool that is mixing and swapping genetic material with the outside world is not unitary enough to be regarded as an isolated, discrete entity. Groups within the species can still be capable of interbreeding, but the species taken as a whole must still be pretty homogenous. (right? Well, that’s what I got from it. If this book had been written for a more general audience, we might not even be having this discussion)

So, if I understand him right, he's effectively saying that if gene-pools are to be regarded as replicators, then it is during the “the crisis times known as speciation events” that the replication occurs, but with a "mutation" (Dawkins doesn’t use the word in this context, but I presume he must be talking about something equivalent to this) that changes some aspect of the gene-pool, which is then restored to equilibrium, (a different one to the parent species, obviously) until the next speciation event (and this is in a more precise sense than the “mutation” I invoked in my prior message, because I failed to take into account homeostasis). Species selection can then judge certain species compared to others, and so some lineages may do better than others, for various reasons, some of them essentially random. He brings up the case of horses in the Tertiary as an example of how a lineage of larger horse could have given rise to today's horses, even though most lineages back in that time were experiencing selection for smaller size. Presumably (he didn't specifically mention it) the reason that the large-horse lineage could have been due to any of a number of possibilities; perhaps larger horses can roam further and are therefore able to reach food more effectively, which would come in handy during droughts and other tough periods. Perhaps larger horses already happened to be more widely distributed than their smaller counterparts, and when a drought or whatever it was did hit, most horses died out, including a sizeable portion of the large horses, but not all of them, and they were able to recover and evolve further, unlike the small ones which were wiped out altogether because of their limited range (this is an example of a feature that belongs to the species but not to individuals of that species; the species itself is widely distributed, but the individuals might only be confined to a limited range). Or it could have been because of something even more arbitrary, say a pathogen happened to hit the small horses where they lived and left the larger horses unmolested. You might even say that species selection magnified what had happened due to natural selection within the large-horse species (a systematic, adaptive trend towards larger size) by making it the basis of future evolution, even while most horse lineages were evolving smaller size before the extinction hit. You can see that size is the type of thing that species selection could act on, and you can see that it is simple. Admittedly, that makes it rather uninteresting compared to, say, the evolution of the vertebrate eye or bat echolocation, but we’ve noted how species selection is not capable of bringing about “progressive evolutionary change”. Anyway, I don’t know much about horse evolution, but my examples of possibilities were meant only as the type of thing that might be invoked to illustrate species selection.

“I get the idea that the concept of species selection annoys him as well, but that he includes it for the sake of fairness, because it seems to be theoretically possible”

Actually, I don’t think it’s so much that it annoys him, though he is undoubtedly fair in his treatment of species selection and bends over backwards to concede the possibility of the variants he doesn’t subscribe to. I think that he is trying to reign in what he perceives to be overblown rhetoric on the one hand, and the residual group selectionist tendencies in many people’s minds that sometimes crop up, even in the scientific literature, on the other.

“The essense of Gould's view was that the individual is the unit of selection, and that is what I took from his writings; it has created a great barrier for me in understanding Dawkins' view, but Dawkins keeps referring to the Necker cube as an analogy for how one can toggle between the concept of the individual and the concept of the individual's genome. I struggle with this, too.”

The Necker Cube, as you know, is a cube that flips back and forth, and either orientation is valid. This is an analogy to the way we can look at life, and that either view is “true”. Gould had it that individuals are the units of natural selection; in his words, selection “accepts or rejects entire organisms because suites of parts, interacting in complex ways, confer advantages.” To Dawkins, the individual might be the immediate, proximate unit of selection, but the gene is the ultimate unit of natural selection, because genes, acting through bodies, can project phenotypic effects on the world and hence have an influence on their prospects of getting copied. Think of this: one orientation of the cube is the traditional, individual-as-unit-of-selection perspective. An organism strives to increase its inclusive fitness. The other orientation of the cube shows that the gene programs its host in such a way as to maximise its chances of getting copied. Both views amount to the same thing; they are approximately equivalent, though there are advantages to adopting the gene-centric view, as it is more “all encompassing” than the traditional view, as there are some cases where looking at the individual as the beneficiary makes no sense (heterozygote advantage is an example). The individual is directly “seen” by selection, of course – it is the entity that actually does the dirty work in the here-and-now, but it is best regarded as a vehicle, a temporary, throw-away device used by the genes that ganged together to produce it. It is definitely not a replicator, for it is not copied. Not even asexual organisms, as we have seen, are copied. I find Gould’s objection to the gene being the true unit of selection, on the grounds that genes cannot be directly seen by it, rather unimaginative on his part, and Dawkins’ retort is perfectly legitimate and fully satisfactory (on p117). The entity that survives the evolutionary process is the gene (and we don’t need to be apologetic about it being judged by proxy. We don’t have to say “it is the ultimate unit of selection despite being judged by proxy”). It’s not that individual selection is wrong; it’s that it’s too limited a view when we’re thinking about what actually matters in evolution. No doubt individuals are players, and Dawkins fully acknowledges this. But they are too temporary.

Dogscratcher asked if the “Central Dogma” can accommodate symbiogenesis. I think it can, but we need to be cautious about how we think about it if we take the extended phenotype seriously. There is a spectrum of symbiosis in terms of intimacy of association between relevant parties: from bees and flowers coadapted to one another, to aphid-farming ants, to Mixotricha that break down cellulose in the guts of Darwin’s termites, to our own mitochondria (originally free living bacteria; interestingly, our nuclear DNA appears to be closer to the archaeans while our mitochondria are closer to the eubacteria – and specifically the one that causes typhus). The difference between our mitochondria-containing cells and the relationship between aphids and ants seems obvious, but in an important way that difference is not as marked as we would at first presume. It’s true that our mitochondria reside inside our cells and aphids reside outside of ants, but the doctrine of the extended phenotype tells us that the effects of genes can reach out into the world. Ant genes that program ants to farm aphids reside inside ants and not aphids, but they co-opt the muscles and other apparatus of aphids nonetheless. Natural selection acted on genes residing inside of both ants and genes to set up this symbiosis; mutually beneficial behaviours arose in both lineages, and the morphology of aphids was also altered in the process, becoming more “domesticated”; in much the same way that genes within a gene-pool work well in the presence of other genes in that gene-pool, so genes that work well in the presence of other genes that happen to reside in another gene pool will tend to get selected. Should the genes residing in aphid bodies therefore qualify as the ant’s “own” genes, and vice versa? That they happen to reside in separate bodies is incidental. Should Darwin’s termite count as its “own” genes those residing in Mixotricha? What of Mixotricha itself, which is a congregation of yet smaller cells, in the form of spirochaetes and pill bacteria attached to a large protozoan? Let’s not stop there: most would qualify mitochondrial DNA as “our own”, even though, evolutionarily speaking, mitochondria is glorified bacteria. But should we hesitate when asked about the organisms in our guts, which help break down food? These micro-organisms don’t live inside our cells, but they do live harmoniously in close proximity anyway, and they might as well have migrated inside some of our cells if the opportunity arose.
Teams of replicators that pass through the same germ-line will tend to develop strikingly intimate levels of cooperation with one another, and whatever conflicts of interest they once had will eventually disappear, as what is good for one will tend to be good for the other. Their vehicles will eventually “blend into” one another, losing parts of themselves as tasks are coopted, even to extreme levels (I think I read that if we were to suddenly lose our mitochondria, we would die in a second).
Maybe you have a point about Lamarckism; it’s certainly an interesting one you raise. I shall have to check whether the book has anything to say about this (it has a chapter dealing with a “Lamarckian scare”, the contents of which I can’t really remember), or whether any workers have taken it upon themselves to answer it. I suppose that, for the subset of symbiotic relationships that involve germ-line sharing, you could sensibly talk about “characteristics acquired during an organism’s lifetime”. I raised the above to alert you to the fact that this would still be a subset and that there is nothing really sacred about it when you think about how evolution works. It might be Lamarckism in terms of the first organisms that happened to be infected with/tried to digest those ancient bacteria and which started to adapt to their hosts/prey after subsequent copyings, but once the symbiotic relationship was underway, it would no longer have made that much sense to talk about separate organisms, because they both shared the same fate and travelled as a unit, so the genes of one could be fairly regarded as the genes of the other. A better example, now that I think of it, could be the immune system: a mother passes onto her infant pathogen resistances not through the germ line per se (the zygote) but via the placenta. Changes accrued during the mother’s lifetime in the form of immunity to certain pathogens is acquired by her infant. The genes of the antibodies could be regarded as the mother’s own for the reasons highlighted above, and then the baby’s own (note that here we’re talking about a gene-pool, as a population of micro-organisms is passed on, and I have only a vague idea of how that would complicate the discussion). I’ll look into this some more, but right now I have to go. But what you said has really spurred me to think about these things more deeply.

Lui said...

Sorry, it meant to read: "Presumably (he didn't specifically mention it) the reason that the large-horse lineage prevailed could have been due to any of a number of possibilities;"

John said...

"There is a causal arrow," writes Dawkins, "going from gene to bird, but none in the reverse direction."

Os so we think we know. Did anyone see this?

Kristine said...

That's an interesting discovery, John, which seems to be in the area of "evo-devo," not something I know anything about (yet). However, as dogscratcher said, perhaps I should revise my statement about Lamarckism because it could be taken to mean something more limiting than I meant it to (I'm an old dog myself, and the information about evolution has changed a lot since I last read Gould!).

But let me make this clear: what does not change during the organism's life is the genome. What is happening in the bird that receives a mother's care is a change (if I am understanding this correctly) in what genes are expressed. However, during the creature's life, broken legs and such do not have effects on the genome so that they could be passed down to subsequent offspring. That is what I mean by Lamarckism.

Lui, I have to read your post again, once I complete all my homework! :) I'm facing another marathon session in the library today.

Lui said...

Hi Krisitine. How are your studies going? If you have any questions, feel free to ask, and I'll try my best to answer them.

Kristine said...

Hi, Lui. I was literally just thinking about you, and feeling a little guilty because I haven't replied for a while.

I'm facing midterms--which means projects. I'm indexing the book Innumeracy: Mathematical Illiteracy and its Consequences for my Indexing and Abstracting class (I can't believe this book has no index!), and learning the database Dialog for my Reference class.

Since I made a dent in my work today (because we had a snow day!), I hope to return to this tomorrow (Saturday), I promise! Thanks for hanging in there.

Kristine said...

I think Dawkins has no problem with a limited form of it, though, it's just that, in his words, "it doesn't seem to do very much".

I agree with you; in fact I think it probably does diddly-squat in the long run.

I haven't gotten through The Ancestor's Tale and so have not grasped "evolution of evolvability"--it makes me a little confused, perhaps "evolution of adaptability" would be a good substitute? (Or would this actually be a different phenomenon?)

Species don’t strive towards cladogenesis, it just happens for arbitrary reasons.

Got it. I agree totally.

I think what he must have meant was that the contingencies that our ancestors found themselves living under were essentially random

Yes, of course. But I think he was also saying that consciousness did not necessarily reveal anything deep and true about the cosmos, and that the evolution of it did not represent a progression or a giant leap forward for nature. It is an adaptation like any other, but it's not the pinnacle of evolution. Therefore, to wonder about the long odds of evolution producing consciousness is no different that wondering about the long odds of evolution to produce any specialized adaptation. In addition, animals have degrees of consciousness; it is we who separate consciousness from the list of unlikely adaptations and wonder about it (because we can!), when in fact who besides ourselves benefits from it (and do we, really, at this point?).

I think that is what Gould meant when he characterized evolution as not progressive, because he saw people, including scientists, imparting a special status and value to consciousness that it really doesn't have. That seems like a harsh statement to make, but it isn't, really.

I agree with you; given billions of years, evolution will accomplish something, but the chances of it creating any one particular thing are small (like the chance that you get a certain hand in poker are extremely small, but nevertheless you will get something, itself quite unlikely).

Lui said...

Hi Kristine. I wrote a response to your latest message but thought better of it by not sending it because I feared that I was distorting both Gould and Dawkins' ideas about evolution being progressive, so I'll just recommend Gould's "Evolution of life on Earth" written for Scientific American (I admittedly haven't read it in full, but it spells out his ideas on the matter) and Dawkins' review of "Full House" in his book "A Devil's Chaplain", called "Human Chauvinism and Evolutionary Progress". In the latter essay, Dawkins basically expounds his own view of progress, talks a bit about his ideas of the evolution of evolvability, and calls Gould to task for adopting a human chauvinist definition of progress that seems almost tailor made to be knocked down. I can provide you with both these articles if you'd like.

It should be noted that both scientists agreed on more than many might have given them credit for. Gould fully accepted that complex adaptations could only come about through the cumulative process of natural selection between individuals (though he apparently wasn't so happy with the notion that genes were the ultimate units of natural selection). Dawkins fully accepts that there is no "aim" towards human-like intelligence (indeed, he flirted with telling The Ancestor's Tale from the point of view of another species, but opted for humans because it would be easier for readers to follow and because of his own human bias, fully acknowledged).

Kristine said...

Thank you. I just read "Human Chauvinism and Evolutionary Progress" and you're right, it helped immensely. I'll get a hold of Gould's article when I can (if you visit the Mother Ship, you'll see me crowing about my midterm. Gould was also a literary nut. :-) )

I must have read this particular chapter of The Extended Phenotype six times! Do you know what my problem is? My "problem" is, despite reading Gould I didn't end up like the "American nonspecialists who unfortunately...get their evolutionary knowledge almost entirely from Gould, [and] have been deeply misled." Small wonder I was confused at the relationship between "species selection" and punctuated equilibrium - I never understood it in the manner that Dawkins criticizes, but in the manner that he describes it! "The theory of punctuated equilibrium itself is gradualist (by Gad it had better be)." Damn straight, Professor Dawkins!

So, I got confused because I was never confused? Well--how confusing. :-)

Groups within the species can still be capable of interbreeding, but the species taken as a whole must still be pretty homogenous. (right? Well, that’s what I got from it. If this book had been written for a more general audience, we might not even be having this discussion)

I've just gotten through that part for the sixth time and I think I, too, get it now--and you're right. (I am a general audience. *wink*) But I think that Dawkins is being careful here to the point of overscrupulousness. I actually don't see species level selection at all. The more I look at it, I don't even see the genome of the asexual stick insect as a replicator, the reason being that, aren't they still subject to genetic mutation?

Kristine said...

{I wanted to save my comment before my crappy connection lost it.)

Random mutation is happening all the time. I think Dawkins is onto something in his description of speciation events, but frankly, it is the selection of the mutuation, and not the mutation itself (which is always happening), that leads to speciation. So, even though a gene-pool can remain stable for a long time, that does not mean that it is not mutating and changing, but that the changes are weeded out, kept to a minimum - until circumstances force speciation - and I don't think that parallels the selfish gene explanation, really. I could be wrong.

What I find interesting about the Necker Cube analogy is that it is itself an abstraction. It refers to, but is not, a real cube. I understand what he is saying, but I find it interesting that he must make an analogy that is itself a two-dimensional representation to make another abstraction, his argument, more sensible. I'm not sure where I'm going with that - remember, my degree is in English literature and not in science - but it struck me that Dawkins is using an optical illusion to explain an abstraction, which says something about our inability to just see reality--really, it highlights the bogusness of the claims of intelligent design theorists who would have us believe that our naive view of the world (it looks designed, so it is) is true when it is false. Michael Behe uses a concrete example, a mousetrap, as an analogy for intelligent design, and it suddenly struck me that I was initially perceiving the Necker Cube as a concrete analogy when it is not. And perhaps that means that we humans can only understand the world, and our own abstractions, in terms of abstractions.
...
Sorry. It's late, and I've gotten off on a philosophical tangent. Thanks for hanging in there, and I'll tangle with the question of the central dogma tomorrow!

Kristine said...

Okay, I need to read what you said about Lamarkism again, because I'm getting mixed up again. (I make things more difficult for myself than they need be - I read more into things than is there - that's why, for example, I never passed calculus when I always excelled at algebra and trig.) But here's Dawkins' definition of Lamarkism from the glossary:

Regardless fo what Lamarck actually said [and for pity's sakes I can't remember anymore], Lamarckism is nowadays the name given to the theory of evolution that relies on the assumption that acquired characteristics can be inherited. From the point of view of this book, the significant feature of the Lamarckian theory is the idea that new genetic variation tends to be adaptively directed, rather than 'random' (i.e. non-directed) as in the Darwinian theory. The orthodox view today is that the Lamarckian theory is completely wrong.

And I believe that it is wrong. I don't think this is referring to the acquisition of mitochondria or to the success of genes in proximity to other, reciprocally successful genes. I'm not sure that I would agree that the existence of genes in another body that appear to cooperate with one's own is "incidental." It is the apparent cooperation that is incidental - which is to say, the genes are not "cooperating" any more than color pixels in a photograph "cooperate" with the black one to produce a color photograph instead of a black-and-white one. The presence of the color pixel changes the overall pattern, and the presence of the aphid genes changes the phenotype of the ants and visa versa, but it changes their genes only by proxy, through natural selection.

However, that may be what you've already said, and I may have simply misunderstood you.

There is something cleansing about thinking about all this, I must say. It is a discipline.

Lui said...

Another way to think of this is that genes are selected for their ability to thrive in the presence of the other genes in the gene pool, over a long time and averaged over all the environments that the gene has found itself in (of course, the gene-pool is one of the most important parts of that environment). In The Selfish Gene, there was an excellent analogy using a team of rowers. Rowers that work well in each other's presence (speak the same language, communicate well, train together etc) will tend to do better than rowers who do perform poorly in each other’s presence.

One of the main criticisms fired at the selfish gene theory presupposes that the theory is too simple in that it disregards the environment. Properly understood, it does nothing of the sort. In fact, we can't even speak about selfish genes without invoking the environment, and that includes, necessarily, the other genes that happen to be present in the gene pool. Environment is absolutely necessary to make the concept meaningful in the first place. Yes, it's true that whole organisms are at the cutting edge of natural selection, but over time it's genes that survive. It's genes that gang together to build bodies, and get replicated. I think we could reasonably learn good evolutionary biology without knowing thinking in these terms, but I can't help thinking that our knowledge would be too limited. Our focus would be fixed on facet of the Necker Cube without us even knowing that there was a Necker Cube.

There’s also something liberating about knowing that we’re the products of a blind process without anthropocentric notions, that we are, ultimately, the survival machines for entities that have no perception of prejudice or other petty human foibles, but which form the basis for them; what a weight off to know that we’re responsible to one another instead of to a supreme being that we could never hope to emulate! That burden seems terribly oppressive.

Kristine said...

Rowers that work well in each other's presence (speak the same language, communicate well, train together etc) will tend to do better than rowers who do perform poorly in each other’s presence.

*More flights of fancy alert* I have been thinking about PE in terms of quantum theory, specifically in terms of wave interference, with periods of "stasis" (even though they're not really) representing the troughs, and speciations the peaks. Is this a plausible connection? Your mention of the rowers made me think of it - I envisioned two sets of rowers becoming, due to circumstances, briefly entangled (this isn't a good image, because boats and rowers don't split off) and their rhythms becoming erratic and chaotic, spurring a speciation event.

I agree that the selfish gene could not exist without the environment, and I cannot understand how anyone could make such an accusation of Dawkins. What do they think he's talking about when he mentions replication? The replicator is successful because it's selected, and it must perform well in its envrionment to do so.

At any rate, thanks for hanging in there, Lui. I've finished the chapter and shall post on it soon.

JohnADavison said...

Dawkins is wrong again. There is probably not a single organism on this earth that is capable of any further evolution. Phylogeny, like ontogeny, has proven to be self-limiting and self-terminating. The extinction of the species is the counterpart to the death of the individual. There is every reason to believe that Homo sapiens is the last mammalian species that will ever appear on the planet.

I agree with Robert Broom that there was a Plan, a word he had the temerity to capitalize. I further contend that the Plan has been realized with the ultimate evolutionary product - ourselves.

All that remains is extinction, the ultimate fate of nearly every species that ever existed. There are no reasonably large "living fossils" and Homo sapiens is very definitely on the large size.

Sorry about that.

It is hard to believe isn't it?

I love it so!

"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison

Kristine said...

Well, John, I remember someone telling me "You could bleed to death and I won't show up [at your blog]," but being that you inadvertently inspired this blog (especially its title), what can I say but thanks for stopping by.

Alan Fox said...

Hi John

You, I see, disagree with Dave Springer's (and presumably Dembski's too, silence giving consent) stance on climate change. I have seen comments from you expressing concern about the environment

Alan Fox said...

Oops pressed "publish" instead of "preview". (Out of practice :))

... about the environment, so you must be pretty disgusted with Springer's attempt to conflate ID with denial of global warming.

John wrote:
Dawkins is wrong again.

The Extended Phenotype is an excellent read for anyone wanting to get a good insight into evolutionary theory, and The Ancestor's Tale a rewarding wide-ranging work that is also a useful reference book for the layperson. You could do worse than emulate his integrity and patience in promoting his views.

BTW it looks like Jason Rennie is back-tracking on publishing your interview, and editing it down to a few "highlights". I was looking forward to the unexpurgated version.

Kristine said...

Hello, gentlemen. Due to our past entanglements I just want to issue a friendly reminder that, unlike at the Mother Ship, Amused Muse (where just about anything goes, except some things, for example if I get too wigged out), this blog confines its subjects to on-topic comments about science. If people want to start a global warming thread I would be happy to. Thank you for visiting.

johnadavison said...

Falan Ox

I have been assured by Jason Rennie tht my interview will appear with little or no editing. I believe it will appear soon. I have no idea where you got the notion that he didn't intend to publish it. Perhaps you will enlighten us. But then perhaps you won't.

I love it so!

"A past evolution is undeniable, a present evolution undemostrable."
John A. Davison

Kristine said...

Do keep the tone neutral, please.

Jason has assured me that I'll be notified when the interview comes out.

johnadavison said...

I am impatiently waiting to hear where Fox got the notion that Rennie does not plan to present my interview. I presume Kristine would join me in that request. Right Kristine?

"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison

Kristine said...

Keep the tone neutral and quit attacking people, or you're gone, and I mean it. Alan Fox has his own blog, as you are well aware, if you want to confront him about this niggling point. It seems that there were many misunderstandings about your interview, which will be cleared up when it airs.

How tired I am of these personal recriminations! This is not your blog. You once told me I was not a lady - maybe you should model the behavior that you want to see in other people instead of criticizing them. Believe me, John A Davison, I have not lacked for abusive and relentless criticism in my life. So take it elsewhere.

johnadavison said...

I am attacking no one. I am simply claiming that nothing Dawkins, Gould or Mayr have ever written had anything whatsoever to do with speciation or the formation of any of the highet taxonomic categories.

All of organic evolution was emergent from within the evolving forms and took place on a predetermined schedule independent of the environment. In a word it was "prescribed" as my 2005 paper claimed. In other words Darwinian evolution is a hoax. Besides, evolution isn't even going on any more beyond the elaboration of varieties, none of which are incipient species in any event.

"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison

Lui said...

"Dawkins is wrong again. There is probably not a single organism on this earth that is capable of any further evolution."

On what basis do you make this extraordinary claim? I happen to know that here in Australia, the evolution of the cane toad (Bufo marinus) is being studied by the CSIRO and The University of Queensland's School of Biological Sciences, and that snakes are evolving ways to cope with the cane toad's venom. Perhaps you should sent them a letter explaining that they're very much mistaken and that they don't know what they're talking about? Note that you said "ANY further evolution". This is demonstrably false. And not only is it false, but the explanation for what we see is utterly Darwinian (and very much dependent - not "independent" - of the environment). And there's no hint of either lineage being affected by the mere fact that we've evolved an extreme level of complexity. This sounds downright mystical.

Anyway, your claim is nonsensical on the face of it because many creatures alive today are much simpler than creatures that were alive during the Mesozoic, for example. If you mean to invoke complexity as the "brick wall" that stops further evolution, then you must explain the evolution of, say, a branch of the theropod dinosaurs – themselves highly complex, arguably sophisticated creatures - into birds, unless you mean to say that birds are a "devolution" of dinosaurs. Perhaps it’s true that there is indeed an upper limit on the level of complexity that is attainable by any species, and that humans have reached this upper upper limit, but that does NOT mean, “evolution [itself] has stopped”. It has no bearing whatsoever on how other lineages will evolve. There are other ways to evolve than to increase complexity, and of course, as I just said, there are plenty of creatures alive today that are pretty simple and don’t come anywhere near the complexity of human beings or even tuataras. Nematode worms spring immediately to mind. Why couldn't they evolve into something more complex over time? Of course, to then say that even they are incapable of further evolution is to invoke some mystical essence or “goal”, for which no evidence exists (and even if it does exist, why should it matter whether other lineages continue to evolve or not? If evolution has reached its "goal" of producing us, how does it follow that evolution will be automatically be curb evolution in all other lineages? By invoking God, I suspect. But then how is this a scientific theory, if you need to make appeals to a mysterous force imputed by a deity that somehow prevents evolution? Those CSIRO guys are doing nicely without it. This IS mysticism, pure and simple). This sounds more like a last desperate attempt to sneak God into the equation. It smacks of an eagerness to find any holes in the theory of evolution by natural selection and stretch them out to hopefully bring the whole edifice crashing down. It won't happen, of course. What you're selling is religion, not science.

"Besides, evolution isn't even going on any more beyond the elaboration of varieties, none of which are incipient species in any event."

How would you know that without the benefit of hindsight? ALL animal species start off - must start off - as "elaboration of varieties". That is the very thing Darwinian evolution predicts, and this is the only way that in principle it could work. An absolutely facetious argument, in other words, not because it's false, but because you present it as somehow fatal to Darwinism. Sorry, but it doesn’t even come close to being fatal. Your caricature - that we should see whole new species in order to accept the theory at all - is completely unwarranted, and I suspect you know it, because you can't be that ignorant of how Darwinian evolution is purported to work.

You might want to look into outbreeding depression. The members of what we’ll provisionally call "sub-species" are capable of interbreeding with members of other sub-species, but their offspring are less viable than they would be had they bred with members of their own sub-species. Natural selection will of course favour those individuals who have less of a propensity to invest time and energy into breeding with members of other sub-species (why wouldn’t it?) and thus squandering opportunities to propagate their genes. This is a beautiful example of incipient speciation, because we can see how an initial starting condition (allopatric processes whereby separated gene-pools accumulate differences, later to be possibly re-united) can snow-ball. Natural selection reinforces the differences among sub-species when – on average - it doesn’t suit the genes of either to mix together. Any gene that predisposed an individual to be more discriminatory towards a potential mate would be favoured to the extent that mixing genes within somewhat different gene-pools is deleterious (perhaps because of genetic or chromosomal incompatibilities or whatever the case may be, which leads to outbreeding depression). The two populations have diverged far enough apart for them to not produce offspring AS viable as they otherwise could, and natural selection is reinforcing this separation. There is nothing I know of that would not eventually make them completely separate, bona fide species that are incapable of interbreeding even if they wanted to, especially since a time will come when they would never even attempt to interbreed. They’ve come this far. Why not a little bit further, and a little bit further still? It is examples like this – which lie within a smooth spectrum ranging from sub-species and varieties, to species within a genus that still hybridise to produce offspring, to species that are so similar to one another that they are arguably “only” sub-species, but which differ in some behaviour that prevents them from swapping genes anyway, to those that produce sterile offspring, to those that can't produce any offspring even if they tried – that are precisely what we would expect to find. These are the types of things we should see if Darwinian evolution is true. Clearly, animals, microbes and plants are still evolving, and every ecologist, geneticist and evolutionary biologist knows it. It’s the focus of a tremendous amount of current research. The “upper limit” to evolution you invoke is fictitious, because all that evolution needs is variability to work on, and some mechanism to effect change within a population (not necessarily natural selection; genetic drift is another possibility). It has both in spades. And it doesn’t matter whether you’re talking about evolution in the Devonian or evolution in the Quaternary, it works the same way. Even entire kingdoms had to start off as diverging populations of a single species, producing separate sub-species thereafter and so on. But of course one wouldn’t know that without the benefit of hindsight if we had been living at the time. How could we?

Then, of course, there are ring species, which, in Dawkins’ words, “strike a blow against the tyranny of the discontinuous mind.”

Kristine, keep on reading Dawkins and Gould. Rest assured that Darwinian evolution is the ONLY theory worth taking seriously right now, and that the only objections left to it are almost invariably religious, which is undoubtedly what we see here.

This might also be worth a look: New species (note that even if ALL these examples are, upon closer scrutiny, only examples of "mere" elaboration of varieties, as you alluded to, we would STILL be obliged to accept Darwinian evolution as the most parsimonious explanation for the complexity of life, given all we known about biology. Talk about “essences” and “Omega points” is the sheerest nonsense).

Lui said...

And here.

Lui said...

A few typos back there.

To go a bit further, think about what a goal directed evolution would look like. If evolution "strives" to produce humans, then shouldn't all lineages have done the same? If evolution is not a mechanical, algorithmic process that differentially sifts through biological outputs and preserves a minority by virtue of their ability to survive and reproduce in the context of the constraints and challenges posed by the environment, but is instead something "emergent from within the evolving forms", should we not see millions of convergent evolutions of Homo sapiens? What about the Ebola virus? Is that also the product of a goal directed evolution? Was that fiendish weasel of a virus also part of the plan? Talk about missing the goal by a mile! I've seen photos of people afflicted with Ebola and Marburg, and let me tell you, these lineages "knew" what they were doing, and it had nothing to do with producing us. They certainly don't care what we think of evolution. They just evolve.

For evolution to all of a sudden stop with the advent of our species, the "message" must somehow have been sent out to all the other lineages to stop evolving. "Okay guys, cut it out now!" But then why had those millions of lineages all gone so far astray from their goal in the first place? We're to believe that it was "independent of the environment". So what was it dependent on? A mystical essence or inner evolutionary complex or whatever you want to call it. Magic, in other words. And horribly contrarian magic, for not only did nearly every single lineage misfire and go down a completely different pathway which had nothing to do with us, they went on to evolve some exquisite adaptations that had nothing to do with the environment but somehow everything to do with the all-important goal of becoming human, which they failed to do. So this inner drive produced things that were completely irrelevant to its purpose. Like the vomiting induced by Ebola and the worm that makes rats run towards their feline predators. These phenomena are comfortably accounted for by a Darwinian view of things, but they make NO SENSE when invoking goal-directed essences.

It's a shame that viruses and harmful bacteria never got the "stop evolving" message. That could have saved a lot of lives and suffering.

johnadavison said...

Darwinism is now in its terminal death throws with Richard Dawkins its last champion. It has been nearly a century and a half of nothing but mass hysteria. It is the biggest hoax in the history of science and Dawkins is now all alone holding the empty Darwinian bag.

On the other side are the IDists led by William Dembski, another loser, who has reinvented Intelligent Design and has even claimed to have proved it mathematically!

It is hard to believe isn't it?

The first IDer was William Paley who claimed, long before Darwin -

"Where there is design there is a designer."

Sorry Paley, but you are wrong also. All that can be said with certainty is -

Where there is design there WAS a designer.

That cannot be denied and that is all that can be substantiated. That is also all that is required by my Prescribed Evolutionary Hypothesis. There is not a shred of evidence for a living God and never has been. That does not mean that such a God does not exist, but it does mean that IT or THEY have no role in science. I know of not a single scientific advance that ever depended on a God of any description.

Christopher Wren designed and rebuilt Saint Paul's cathedral. Wren is dead and the cathedral remains. Need I say more? Get it? Probably not.

"God is dead."
Frederich Nietzche

Right on Fred!

And so you see both sides of this idiotic debate are dead wrong.

Naturally,

I love it so.

As for the rest of you Darwinian mystics, go right on worshipping Dawkins, the last champion of the biggest and most long-lived hoax in the history of science. It has been nothing more than nearly a century and a half of sustained mass hysteria, produced and then perpetuated by generation after generation of those poor souls who were "prescribed" to be congenital atheists.

Einstein put it this way -

"Then there are the fanatical atheists whose intolerance is the same as that of the religious fanatics, and it springs from the same source... They are creatures who can't hear the music of the spheres."

and

"Everything is determined... by forces over which we have no control."

You now have my permission to continue with your cozy litte "groupthink."

Ask not for whom the bell tolls. It tolls for Godless Darwinism, the biggest joke in the history of science.

"A past evolution is undeniable, a present evolution udemonstrable."
John A. Davison

Kristine said...
This comment has been removed by the author.
Kristine said...

Lui, check here for some context:
http://amused-muse.blogspot.com/2006/09/genetic-algorithms-for-uncommonly.html#c115771725486356226

Paste the link in your browser - everything will become clear then.
;-)

Another post coming soon, I promise.

Lui said...

"Darwinism is now in its terminal death throws with Richard Dawkins its last champion."

Sorry, I hadn't noticed this world-shaking development.

"It has been nearly a century and a half of nothing but mass hysteria."

I think you're talking about creationism there. Scientists aren't in the business of hysteria.

"It is the biggest hoax in the history of science and Dawkins is now all alone holding the empty Darwinian bag."

Really? That's strange, I could have sworn that Sean B. Carroll is also a prominent Darwinian, as is Ken Miller, Robert Trivers, George C. Williams, Stephen Pinker, Daniel C. Dennett, every population geneticist I've ever heard of, as well as every ecologist working at my university.

"Christopher Wren designed and rebuilt Saint Paul's cathedral. Wren is dead and the cathedral remains. Need I say more? Get it? Probably not."

Yes, I get it. You prefer arguments from personal incredulity to rigorous scientific scrutiny.

"As for the rest of you Darwinian mystics, go right on worshipping Dawkins,"

No one's worshipping anyone. Dawkins is one of many Darwinian proponents, and in any case it's not in our nature to worship (personally, I've never even prayed in my life). Clearly you have no conception of the word "mystic" either, or else you'd see how well the word applies to the concept you're proposing.

"the last champion of the biggest and most long-lived hoax in the history of science."

And what, I wonder, is the purpose of this "hoax"? Is every ecologist out there part of some giant conspiracy? Honestly, is this some sort of a joke?

"You now have my permission to continue with your cozy litte "groupthink.""

Thanks.

Since this is supposed to be a scientific discussion, I would appreciate some scientific objections to the points I raised.

Kristine, I just don't know what to make of it. I found it almost heart breaking, and I feel somewhat guilty posting all of the above. But here's a link in case you haven't seen it: Davison.

I also skimmed through his article article An Evolutionary Manifesto and I found this: "Perhaps the most compelling feature for the Darwinists resides in their persistent conviction that all of evolution is the result of
blind chance."

I mean, really. Who says this?

"Stephen J. Gould has recently compared the evolutionary process to a drunk reeling back and forth between the bar room wall and the gutter (1996, page 149). He has also described intelligence as an "evolutionary accident". I will only say that it was some accident!"

Such an objection is not one that could possibly be made by someone who understood what Gould was trying to convey. Despite our confusions, I think that you and me, Kristine, have discussed this very issue with far more insight and sensibility. We both at least know what Gould didn’t mean.

"Richard Dawkins' Selfish Gene, Blind Watchmaker, and
Climbing Mount Improbable require no further comment from me."

Is this the glimmering of a God-complex (especially since he hadn't even commented on any of the three books in the article)?

Kristine said...

Since this is supposed to be a scientific discussion, I would appreciate some scientific objections to the points I raised.

Lui, evolution truly will come to an end before you get an answer! ;-)

It breaks my heart, too. But he's actually behaving himself here so whatever, I'll let him spout.

This "evolution is finished" stuff seems to be his unique take on a "theory" that I've heard before, that being that the universe is "winding down." Usually the proponents are anti-evolutionist physicists.

johnadavison said...

Sorry kristine but you won't "let me spout." I have washed my hands of your mindless little Dawkins fan club. Enjoy one another. I have much better things to do than to try to educate evolutionary illiterates. Richard Dawkins is a "prescribed," congenital, homozygous loser.

"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison

Kristine said...

Well, thanks for being a good sport and take care of yourself John.

Lui said...

You're yet to refute anything I said John. Judging by how you misrepresented Gould, I would say it's you who's in need of being educated.

Kristine said...

Lui, shhhh! Let him go. ;-)

I'm glad it went as well as it did. He was really restrained here, after I laid down the law. John can get quite vituperative and I didn't want that.

You're not going to convince him. It's beyond argument; health issues, cognitive, I don't know what it is. (I'm trying to say this nicely.) In a way I love the guy.

johnadavison said...

Kristine.

Alan Fox has banned me from posting on his shabby little blog just vas David Springer has on Uncommon Descent. They are each nothing but hired goons for their masters. Wesley Elsberry and William Dembski respectively.

The reason I am banned is because these clowns are scared to death of me and my sources. If they have the balls they may communicate with me either on my blog or at Brainstorms.

I sure as hell am not going to interact with either of these phonies here on your blog. They can both go to hell as far as I am concerned.

"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison

Kristine said...

David Springer does not come here as he has agreed, as a gentleman, not to visit my other blog anymore. I wish you would show the same restraint and gentlemanliness and quit baiting people here in an obvious attempt to draw them in.

You are not banned, but unless you have a point, make with the bye-bye.

johnadavison said...

This is for you Dawkins fans,

https://www2.blogger.com/comment.g?blogID=4412672427182333335&postID=7556043756485780134

Comments #14 and #15

Enjoy!

A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison

johnadavison said...

I do not bait my several adversaries. They are much too cowardly to show up. I simply expose them as the mindless ideologues that they all are. It gives me pleasure to do so. Now go read some more Dawkins, the biggest charlatan in the history of evolutionary science.

"Study Nature not books."
Louis Agassiz

Got that? Write that down.

"A past evolution is undeniable, a present evolution undemonstable."
John A. Davison

Kristine said...

I certainly shall read more Dawkins. Good idea. I daresay considering your behavior people fear for you rather than fear you.

Lui said...

You're right, Kristine. This guy's lost it. I "showed up" to his blog, posted a lengthy rebuttal to his nonsense, and what did he do? Like the great scientist he is, he deleted my message (the very thing he complained about others doing to him). Not even the most ignorant fundamentalists have deleted my posts from their blogs. I hope he enjoys talking to himself.

Kristine said...

He does. ;-)

Don't let it get to you, Lui. This stuff goes way back. He's deleting everything from his blog, because he thinks he's been banned from Alan Fox's blog when he's not (but he was banned from Uncommon Descent - I saw the comment that did it, I will not repeat it because it's icky, and I agreed with DaveScot for kicking him off). So now he's getting his "revenge." Let him. He's an old man and frankly, as I said, it's a mental illness.

Alan Fox said...

You are an incredibly charitable person, Kristine.

Aside to John:

You have never been, are not, and will never be banned from my blog, no matter how hard you try, so there!