Are Genes Alive?

[jackdavinci]

[QUOTE=Stranger On A Train]
Virus do not self-replicate, nor do they metabolize.
[/QUOTE]

Yes, we agree that viruses have some unique features that other classes of organisms differ with - but that is true of all organisms. Usually those features are used to categorize them as different species for small differences, or kingdoms for very large differences. We could just as easily classify viruses as a seperate kingdom of “life” rather than putting them outside of “life” altogether. The current technical/scientific definition has certainly evolved over time - the concept of alive/living has existed far far longer than we have known about cells.

So certainly, yes, the current definition for “life” is a useful classification set of some important phenomenon. But certainly it’s an arbitary (arbitrary as in “not inhernently essential”, not as in “without consideration”) place along the continuum of life-like phenomenon to put a dividing wall. Certainly this class of phenomenon is important and should have a label, but it’s far from a given that this is the set that we should correlate with the term “alive”.

[QUOTE=Stranger On A Train]
Outside of these cells, they are essentially biologically inert
[/QUOTE]

Many spores are inert outside of their perferred environment.

[QUOTE=Stranger On A Train]
metabolism and self-replication are fundamental in the definition of life.
[/QUOTE]

They are fundamental to a certain class of phenomena/organisms, which modern science has come to attribute the term “living” but they are certainly not fundamental to the concepts of “living/alive” as they were originally and still continue to be understood.

[QUOTE=Stranger On A Train]
We may be a little hazy in some examples as to what completely satisfies the conditions for life, but viruses clearly do not meet any standard for independent life.
[/QUOTE]

The fact that you have to qualify “life” with “independent” suggests that “independant” is not an inherently necessary quality of “life”.

I frankly don’t understand your point about crystals or fire having “life-like” traits; it is clear that these, too, are not alive in the sense of having and reproducing a complex structure which moderates energy flow to power its own processes and is robust in resisting alteration to structure. Viruses at least have a structure, and some even have a limited ability to catalyze the production of simple proteins, but none can reproduce their own structure in toto without hijacking the processes of a cellular organism.

Again, the fact that you have to qualify “alive” with “in the sense of” implies that there are other senses in which things can be considered “alive”. I find it amusing that you argue against crystals and fire being “life-like” by basically stating that they don’t meet every single of your requirements for life, thereby suggesting that they do in fact have some of the requirements, and am even more amused that your second argument amounts to the fact that viruses, while not living, are more life-like than crystals and fire!

My point was not to suggest that crystals or fire meet your requirements for life (I’m not sure why you include “resisting alteration to structure” as this would seem to invalidate another requirement) but to illustrate that there’s a whole range of phenomena that exhibit properties that seem life-likeas “living” was originally and continues outside of science dictionaries to be concieved.

[QUOTE=Stranger On A Train]
I find it very difficult to conceive of an alien species that is not in some fashion built around a cellular organization.
[/QUOTE]

I don’t find arguments from lack of imagination very convincing or useful.

[QUOTE=Stranger On A Train]
Any complex self-organizing system implicitly has a cellular structure.
[/QUOTE]

I think this is paramount to a tautaology. Anything that is self-contained is in that sense cellular. If there was any species in which there weren’t clear boundaries between individual members of the species, then you would just call the entire species one cell since that was the smallest identifiably distinct unit. So what happens if you divide the species-cell in half? Aren’t there two “cells” now? This is analogous to colony organisms. Is the organism the individual cells or is it the colony?

My overall point is that there are more things that have living qualities than are contained in the modern definition of “alive”, and the modern definition of “living” is more accurately described by using other terminology, so this particular choice is somewhat arbitrary and deceptive.

Further, what’s important here is, in terms of the OP, is that giving a technical answer (the modern scientific definition limits “life” to the cellular level or above) gives us only information about a classification and says nothing about the conceptual problem itself. I think in this particular case, Dawkins was using the term in the “located at” sense. If he was using the term in the strict modern scientific sense then it would indeed seem incorrect. But if he was, or if we were, using it in the general sense - I think that’s an important, interesting, and valid question, that has yet to be answered, and may not be answerable, but reveals much in the dialogue that emerges.

[Stranger_On_A_Train]

[QUOTE=jackdavinci]
So certainly, yes, the current definition for “life” is a useful classification set of some important phenomenon. But certainly it’s an arbitary (arbitrary as in “not inhernently essential”, not as in “without consideration”) place along the continuum of life-like phenomenon to put a dividing wall. Certainly this class of phenomenon is important and should have a label, but it’s far from a given that this is the set that we should correlate with the term “alive”.
[/quote]
If you want to redefine the term “life” to mean whatever it pleases you to mean then certainly you can categories viruses as being alive. You can also categorize digital watches, bodies of water, and breakfast cereals to be alive, too, if you’re willing to exert that kind of intellectual acrobatics. But the fact remains that while we may have a great deal of interpretation on the qualities that are sufficient to characterize something as being alive, there is a well-accepted set of non-arbitrary criteria to satisfy the necessity of being considered as living. By any accepted standard, viruses are certainly not alive, a conclusion supported by consensus of the vast majority of virologists and molecular biologists.

Regarding the expectation of cellular organization in any form of life, it is the case in every complex, self-regulating thermodynamic system that we look at, whether alive, uncertain, or clearly inanimate is organized along cellular principles. The study of this phenomenon is called cellular automata, and it appears all over nature on essentially every scale. It would be astonishing to find any system sufficiently complex to be regarded as alive without displaying a high degree of differentiation into some analogue to cells and subcellular structures. You may regard this notion as being arbitrary or a tautology, but you’re at great odds with even the most speculative thinking about conceptual extraterrestrial life on that issue.

Stranger

[Darwins_Finch]

[QUOTE=Stranger On A Train]
I don’t have handy my copies of The Selfish Gene and The Extended Phenotype to cite from, but I’m pretty confident that even Dawkins doesn’t argue that the focus of selection are genes (except in very special instances where the physical form of the genome is directly acted upon by some enzyme or phage), but rather that the gene is inarguably the physical unit of inheritance.
[/quote]

If that’s the case, then I’m not sure either you nor he (nor anyone else) can criticize Gould for calling a blatantly obvious idea a “new theory”!

Selection, in his view (and the view of most gene centric theorists) acts upon the phenotypical expression of genes, singly or in combination, and that a sufficiently broad definition of phenotype can encompass all higher order categories, from individual functional units of a cell, organ, organism, kin, or group, and by adopting this approach it is, at least in theory, possible to reduce selection upon phenotypical attributes at all levels to their effect on the genome. From the bottom up view, this means that the individual gene “competes” with other genes to be successfully expressed in some form that benefits the carrier and leads to propagation of the gene. Thus, there’s nothing non-Darwinian about it; it just applies an underlying mechanic to the traditional Darwinian approach of viewing competition between organisms or higher groups.

The “bottom up” view, in this case, serves only to muddy the waters; it actually doesn’t clarify anything. Having to introduce concepts about “genes competing” is simply taking the idea that evolution via natural selection is the result of individuals competing for resources to a ridiculous extreme.

I’d like to think the same about evolutionary biology and the mechanics of natural selection; that rather than occuring as distinct processes on different and somewhat arbitrary levels, that there is a single set of underlying principles at the root level of inheritance upon which selection fundamentally acts.

On the other hand, I don’t believe that selection does work, at least not primarily, and certainly not wholly, on the root level of inheritance. It acts upon any given entity – be that entity a gene, an individual, or a population – in the same way. That is, the underlying process of selection works the same way no matter the entity being selected. No need to reduce everything to the genic level, as the process itself is already fundamental.

Talking about kin selection, group selection, organism selection, and so forth as if they are distinct processes that are disconnected (which is, perhaps incorrectly, the impression I get from many texts) strikes me as handwaving, a denial that there is a more fundamental and quantifiable process which dictates how these observable processes occur.

The problem here is that there is a common misconception about “microevolution” vs “macroevolution”. Many will say, “but they’re the same thing! It can all be explained via natural selection!” Well, no. There are certainly macroevolutionary concepts whcih aren’t easily explained using “competition between varying indivudals for resources”. Cladogenetic speciation, for example, is not easily understood solely from the perspective of natural selection; there must be an additional event, or events, by which two populations become separated in the first place, for example. Mass extinctions and the evolution of novel structures are also common macroevoutionary ideas.

Punctuated equilibrium strikes me less as a well-defined hypothesis than a series of interpretations. Even from the writings of Eldredge and Gould I’m not entirely clear on what they believe to be the fundamental cause; at least in the case of Gould, he suggested a number of different causes that were at least somewhat at odds with one another.

Punctuated equilibirum seems to be one of the most misunderstood theories in evolutionary biology, methinks. Ultimately, it’s an explanation for the appearance of the fossil record, not a theory for some new and different process. Indeed, it’s because of the way those processes work that the fossil record appears as it does: lineages appear suddenly and often fully-formed, remain relatively static throughout their lifetimes, then disappear from the record. That is, the lineages appear to be in equilbrium, punctuated by periods of rapid change. And the reason the fossil record appears that way is because of how speciation works. To wit, populations split and diverge; however, often the split occurs because a population subgroup becomes reproductively separated from the parent. That population, being initially small, will yield few, if any, fossils. It’s only when the population becomes established that the likelihood of fossilization becomes high enough to actually yield fossils (assuming the various other criteria for fossilization are met). So, when we first see that population in the fossil record, it appears “done”; we don’t see the rapid periods of change between “small, peripheral population” and “large, well-established population that is clearly a new species”. Once the species does appear in the record, it appears static because the resolution in the record is so crappy. We don’t get to see seasonal variations, or subtle shifts in the population as gene frequencies vary throughout the population like we might if were to observe the process in real time. As such, we typically don’t see a gradual reduction of the population, either: it simply dissappears form the record. And, again, this is for the same reason that we saw it suddenly appear: as the population size decreases below a certain threshhold, the likelihood of fossilization decreases, thus the number of fossils left by the population decreases dramatically.

And really, that’s the main thing about PuncEq. I could never figure out why it has been so villified, to be honest. One of the natural consequences of this idea is that we cannot ever expect a “perfect” record. Quite contrary to Darwin’s idea that if only we could extract every fossil ever formed we’d have a perfect record which would silence critics, as we’d see a clear progression of lineages.

[SiXSwordS]

[QUOTE=Stranger On A Train]
I don’t have handy my copies of The Selfish Gene and The Extended Phenotype to cite from, but I’m pretty confident that even Dawkins doesn’t argue that the focus of selection are genes <snip>
[/QUOTE]

I scanned through the posts since my last post and I don’t think I’ve seen this addressed.

pg 28.

A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.

I’ve gotten mixed results from the link depending on the computer I’m using. I simply searched inside using the Amazon.com feature and used unit of selection as a phrase.

The quoted statement is pretty clear, but the other phrases that come up from that search indicate that this idea is fundamental to Dawkins thesis.

[jackdavinci]

[QUOTE=Stranger On A Train]
If you want to redefine the term “life” to mean whatever it pleases you to mean then certainly you can categories viruses as being alive.
[/QUOTE]

My point is that the term has already been redefined (or rather, been given additional definitions, since the original ones remain valid in other contexts) many times. to “please” scientists. It is therefore inherently arbitrary.

[QUOTE=Stranger On A Train]
But the fact remains that while we may have a great deal of interpretation on the qualities that are sufficient to characterize something as being alive, there is a well-accepted set of non-arbitrary criteria to satisfy the necessity of being considered as living. By any accepted standard, viruses are certainly not alive, a conclusion supported by consensus of the vast majority of virologists and molecular biologists.
[/QUOTE]

That’s circular reasoning. You can’t have a label defined specifically to disinclude certain sets of things, and then claim that the “fact” that those things don’t fit in that category is somehow meaningful.

If you are creating a filing system and your group decides that by convention you will file all filenames with a number in them as their spelled-out equivalent (file 56 as “fifty-six”) and will ignore spaces for the purpose of alphabetizing - it doesn’t mean that the number 56 “really” belongs near “fife”. It just means that it’s a shared convention for handling information.

Nothing about the nature of Pluto changed when astronomers voted it off the “planet” list. All that changed was the formal definition of “planet”.

[QUOTE=Stranger On A Train]
Regarding the expectation of cellular organization in any form of life, it is the case in every complex, self-regulating thermodynamic system that we look at, whether alive, uncertain, or clearly inanimate is organized along cellular principles.
[/QUOTE]

Really? Have some non-biological examples?

[QUOTE=Stranger On A Train]
The study of this phenomenon is called cellular automata, and it appears all over nature on essentially every scale.
[/QUOTE]

Since all biological organisms on Earth are related to each other and have a common ancestor, it is rather unremarkable that they would share similar features.

[QUOTE=Stranger On A Train]
It would be astonishing
[/QUOTE]

The ability to surprise one person with rigid views is hardly an argument for anything.

[QUOTE=Stranger On A Train]
some analogue to cells and subcellular structures.
[/QUOTE]

Cells and subcellular structures outside of the strict biological sense, are basically equivalent to mathematical sets. Since everything in the universe can be ordered into sets, this is hardly remarkable. This will depend on your ability of course to do “acrobatics” with regard to how loosely you define “cell”.

[QUOTE=Stranger On A Train]
You may regard this notion as being arbitrary or a tautology, but you’re at great odds with even the most speculative thinking about conceptual extraterrestrial life on that issue.
[/QUOTE]

That’s frankly impossible. You can’t seriously claim that there has never in the history of man been speculation about extraterrestrial life that doesn’t fit the contemporary definition. On the contrary, it has been my experience that when scientists talk about extraterrestrial life in public forums that they always stress the importance of not falling into the trap of Earth-centrism. That when searching for, or theorizing about other forms of life, it’s paramount to investigate both Earth-similar and possible disparate forms of biology.

In any case I think you are too caught up in forgetting the difference between physical facts and categorization. What happened in certain eras on Earth for example, is more or less proven fact. But the manner in which we divide the history of the planet into different eras, while based on useful criteria, still ultimately is arbitrary and categorical. Dinosaurs aren’t “Jurassic animals” as though Jurassicness were some essential quality of the dinosaurs. It’s more correct to say that certain dinosaurs lived during a period of time we have labeled by convention the Jurassic.

Another example - there was a time when all animals that swam in the water and had tails and fins were called “fish”. We eventually figured out that some of these animals (dolphins, other whales) breathe air and were actually evolved from land animals and recategorized them as mammals. Nothing about the dolphins or the other fish has changed. All that has changed is that we have constructed a new categorization system, and have borrowed some of the original terms for the new system, but give them a new, more limited definition. This doesn’t mean that the old sense of the word is now incorrect. If you read an old book that uses the term “fish” it is not wrong to recognise that the term in that context means “aquatic animals with tails and fins”, and not the same sense as the modern taxonomy term.

One might expect you to say something puerile like “by any accepted standard, dolphins are certainly not fish, a conclusion supported by consensus of the vast majority of taxonomists and marine biologists.” But this would be to ignore all previous history of taxonomy, for a much longer period of time during which dolphins were in the category of “fish”, which had a different taxonomic definition at that time. Don’t confuse convention with meaning.

[SiXSwordS]

[QUOTE=jackdavinci]
<snip>
I think in this particular case, Dawkins was using the term in the “located at” sense.
[/QUOTE]

See Post #8 and try replacing to live with located at

Our DNA is located inside our bodies.
—A bit prosaic, but true.

[T]he genes in the world have an expectation of being located that must be measured not in decades but in thousands and millions [of years].
—If you can make sense of this sentence using the idea of location and reconcile the result with Dawkins apparent IQ of something over 60 I’d like to see it.

But a DNA molecule could theoretically remain located in the form of copies of itself for a hundred million years.
—This is plainly nonsense in this form.

The last sentence is, however, a good indication that Dawkins is playing fast and loose with some definitions. Living in the form of a copy of oneself clearly implies something other than life as we know it.

[Stranger_On_A_Train]

[QUOTE=Darwin’s Finch]
Punctuated equilibirum seems to be one of the most misunderstood theories in evolutionary biology, methinks. Ultimately, it’s an explanation for the appearance of the fossil record, not a theory for some new and different process. Indeed, it’s because of the way those processes work that the fossil record appears as it does: lineages appear suddenly and often fully-formed, remain relatively static throughout their lifetimes, then disappear from the record. That is, the lineages appear to be in equilbrium, punctuated by periods of rapid change. And the reason the fossil record appears that way is because of how speciation works…And really, that’s the main thing about PuncEq. I could never figure out why it has been so villified, to be honest. One of the natural consequences of this idea is that we cannot ever expect a “perfect” record. Quite contrary to Darwin’s idea that if only we could extract every fossil ever formed we’d have a perfect record which would silence critics, as we’d see a clear progression of lineages.
[/QUOTE]
I think we’re going to have to agree to disagree–again–on the topic of gene-centric selection versus higher level selection (though I’ll readily admit that it doesn’t yet provide an explanation for selection on all levels) but I’ll agree almost completely with the above. Unfortunately, some proponents (although not Williams and, as far as I can tell, Gould) have proposed mechanisms (often implicitly or explicitly teleological) for PE that are not valid or supported by evidence or substantial theory, although I find some of Gould’s stated arguments either suspect or confusing (or perhaps I don’t understand them).

PE (or, at least the massive global rate change of speciation at identifiably points in the fossil record) is one of the most interesting areas of study in evolution, because it diverges dramatically from what Darwin, in his time (and lacking anything like a comprehensive fossil record we enjoy today), theorized about the gradual progression of evolution and implies that selection is not a constant, even pressure but changes dramatically in rate given alterations in selective pressures, something that is obvious today (on the microscale, at least) in experiment and from applied game theory. However, I don’t think it should be considered a special and unique process or (from a selection level) even unique type of event distinct or discrete from “normal” natural selection; it’s just a case in which the differences in capability and adaptability between competing species and organisms within a species are magnified by a dramatic alteration in selective pressure. One might equally observe that we’re going through a period of punctuated equilibrium right now; the evolutionarly rapid expansion of Homo sapcies and accompanying industrialization and pollution is resulting in dramatic effects on many species, and as a result some thrive while many more become extinct.

[QUOTE=SiXSwordS]
I scanned through the posts since my last post and I don’t think I’ve seen this addressed.

A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.

…snip…

The quoted statement is pretty clear, but the other phrases that come up from that search indicate that this idea is fundamental to Dawkins thesis.
[/QUOTE]
Dawkins believes–and more generally, the central premise of the gene-centric theory evolution promotes–the notion that all selection boils down to competition between and among genes. Now obviously genes aren’t out there elbowing each other out of the way for resources; except in the rare and esoteric situations in which some kind of selection pressure acts upon the genome, the selection occurs at the level of an organism in which the gene (or combinations of the gene) are expressed as phenotypes (features or behaviors). This is well and good as far as dealing with the active coding part of the genome, but much of the genome of virtually all organisms is inactive, yet requires maintanence and takes resources. Either it’s the case that selective pressures on the genic level are light enough that it’s acceptable to carry around a mass of useless, non-coding nucleotides (doubtful, since viruses, which have to sneak in under the radar and prevent detection tend to minimize all non-coding sequences), that the supposedly non-functional sequences actually have some other purpose (prevent mutation, protect from damage, et cetera), or that genes have their own interest in mind (so to speak) and hijack organisms to carry them around and reproduce them, sometimes in cooperation with the organism and other genes, but most of the time with a sufficiently marginal impact that it’s not “worth it” to the organism or other genes to clean them out. The genes that are most successful, of course, are the ones that make their hosts successful, or at least manage to ride along with a successful host and preserve their form.

The mistake that is often made when regarding gene-centric theory–and one that is amplified by the unfortunate choice of metaphor of “selfishness” and the accompanying miscomprehension (sometimes seemingly deliberate, in the case of critics like Mary Midgley)–is that genes have some kind of volition, or actively participate in the process of being selected, rather than being considered in terms of their empircal utility and attendent likelyhood of being propagated by carriers. Gene-centric theory is ultimately a passive game theory…er…theory, where the advantages provided by a gene to its carrier–where the focus of selection takes place–determine its likelyhood of being successful. This is complicated by the fact that genes are not phenotypes and are not always expressed the same way, and in fact a given gene sequence may be found elsewhere performing some very different function than it did at inception, or may only function in partnership with other independent genes, and in fact most “genes” may not function at the organism level at all (or at least perceivably) but may provide an advantage at a higher organzational level. The social hymenopterans like bees, for instance, demonstrate altruistic behavior that does not at all benefit the sterile organisms but is a benefit to the hive or kin as a whole. This is explained via kin selection (albeit, in my view, incompletely), but can also be demonstrated by looking at the contribution of genetic material; individual organisms are programmed to behave altruistically because it is a benefit to the collection of genes as a whole, while the contribution of individual genes still provides impetus for competition between kin.

One can demonstrate this, albeit with far less discrete and definitive result, in more complex species, too. However, because of the more complex behavior, interaction and competition on various levels, and the variation of socially-learned behavior, it’s far more difficult to show a clear result, and it’s a mistake (as many people, and particularly readers who take home only a superficial understanding) to accept this as being the exclusive influence on phenotypical development and social behavior. As I recall, Enron CEO Jeff Skilling cited The Selfish Gene as his favorite book and a model for his behavior which demonstrates only how ignornant he was of the central premise and application of metaphor. (I personally doubt he read with comprehension past the forward, or perhaps even the title.) I think Dawkins in particular overreaches, or at least speculates without firm foundation at times–he certainly extends out further than George Williams did on the emphasis of “extended phenotypes”–but the general notion of the unit of selection boiling down to inert, strictly biochemically mechanical function of genes is one that clarifies the action of evolution in my admittedly dilettante opinion.

Ultimately, I think gene-centric theory is more of an interpretation than a diametrically-opposed, competing theory with modern evolutionary synthesis and Mayr’s definitive interpretation of modern evolutionary biology. Mayr, of course, would have strenuously disagreed with this, but Mayr was also a stringent opponent of the utility of molecular biology, reductionist genetics, and the application of physics and mathematical modeling for use in explaining selective processes. He seemed to feel–and I’m sure that Darwin’s Finch will correct me if I’m mistaken–that there was something special and unique about life that differentiated from the nonorganic processes of physics elsewhere. This might have been a credible argument in his early days, but I think that the discovery and understanding of the functioning of the genome by Watson, Crick, Wilkins, and Franklin–three of the four of whom had their formal training in physics, not classical biology–has put paid to the notion that there is something fundamentally different about biological processes, and that cells, proteins, and enzymes follow the same physical principles as inanimate material.

Anyone who takes “selfishness” or other statements of apparent intent or ontological descriptions as being equivilient to volition or planning is misinterpreting the metaphor, and its unfortuante that we don’t have a less polarizing jargon to speak of selection and competition. Similiar is the case in quantum mechanics, where the misuse of the notion of “waveform collapse” and “observation causing action” has resulting in unlikely explanations like the Consciousness Causes Collapse or Many Minds interpretations.

Stranger

[Darwins_Finch]

[QUOTE=Stranger On A Train]
Unfortunately, some proponents (although not Williams and, as far as I can tell, Gould) have proposed mechanisms (often implicitly or explicitly teleological) for PE that are not valid or supported by evidence or substantial theory, although I find some of Gould’s stated arguments either suspect or confusing (or perhaps I don’t understand them).
[/QUOTE]

That’s the part I don’t get: the mechanism is already as stated – the nature of cladogenic speciation. That, coupled with the inherent biases of fossilization, both in terms of the extreme unlikelihood of it occurring in the first place coupled with certain environments being more conducive to the process, explains everything quite nicely, in my opinion. I think if Gould errs in presenting or defending PE, it’s by overexplaining.

However, I don’t think it should be considered a special and unique process or (from a selection level) even unique type of event distinct or discrete from “normal” natural selection; it’s just a case in which the differences in capability and adaptability between competing species and organisms within a species are magnified by a dramatic alteration in selective pressure.

It appears here, though, that you seem to misunderstand PE. It isn’t a special evolutionary process; it’s a linkage between the appearance of the fossil record and known evolutionary processes; that is, the fossil record looks the way it does because of evolutionary processes. It says nothing new (or at all, for that matter) about selection, proposes no new evolutionary mechanisms, and is rather silent on the topic of natural selection. It’s an answer to the question, “why does the fossil record look like that?”, not “how does evolution work?” or “how does differential survivability of species lineages work?” Natural selection is plugging away during the entire process, ultimately driving it in the form of adaptation and, coupled with environmental changes relative to populations, speciation.

One might equally observe that we’re going through a period of punctuated equilibrium right now; the evolutionarly rapid expansion of Homo sapcies and accompanying industrialization and pollution is resulting in dramatic effects on many species, and as a result some thrive while many more become extinct.

Again, though, I wouldn’t consider that as an example of PE. To me, PE is only applicable to fossil assemblages. We are going through a period of large-scale extinctions, certainly, but this only relates to PE to extent that those extinctions are recorded in the fossil record for posterity. The nature and causes of extinction itself is not part of PE (at least, not as I’ve seen it formulated).

Anyone who takes “selfishness” or other statements of apparent intent or ontological descriptions as being equivilient to volition or planning is misinterpreting the metaphor, and its unfortuante that we don’t have a less polarizing jargon to speak of selection and competition.

The problem being that it requires an inaccurate metaphor to explain genic selection as a universal phenomenon; you practically have to consider genes to be alive (to bring this thread full circle), or at least treat them as if they were, in order for the metaphor to make any sense at all. Actual examples of “selfish genes” can be found, and described, without resorting to metaphor at all. For example:

If a gene allele is statistically more frequent within an organism’s gametes, and that frequency is similar throughout individuals possessing the same allele, then that gene can be considered a “selfish gene”, even if (or, especially if) the higher frequency of that gene results in reduced fitness for the organism. However, that cannot be said to be the case for all genes. Furthermore, “selfish genes” are often “checked” by individual selection; if the overall fitness of too many members of the population suffers, the population may well go extinct.

Note, above all, though, that there is nothing in it for the gene either way. There is no need to resort to verbiage which implies that the gene “wants to” or “needs to” survive. It is what it is, and it does what it does. There is no theoretical reason why a gene could not be “selfish” enough to cause the entire population, and thereby itself, to go extinct. There is no overarching “need” for survival. Again, though, such often doesn’t happen because genic selection is not the whole story; individual selection will very often place limits on how frequent a given allele, particularly a “selfish” one which decreases individual fitness, can become within a population. Those individuals who may be free of the “selfish” allele could be actively selected for by natural selection, for example.

As such, I see genic selection as a tool, rather than the whole toolbox. I also see, as you may have noted, genic selection is a distinct form of selection from natural selection (possibly a reversal from some previous posts I’ve made here – I don’t recall how I’ve phrased it in the past – but I’ve been thinking upon this a bit more of late).

[Stranger_On_A_Train]

[QUOTE=jackdavinci]
My point is that the term [life] has already been redefined (or rather, been given additional definitions, since the original ones remain valid in other contexts) many times. to “please” scientists. It is therefore inherently arbitrary…Nothing about the nature of Pluto changed when astronomers voted it off the “planet” list. All that changed was the formal definition of “planet”… Really? Have some non-biological examples [of non-animate cellular organization]?..The ability to surprise one person with rigid views is hardly an argument for anything…Don’t confuse convention with meaning.
[/QUOTE]
I’ve abridged and added (in block parenthesis) clarification for the purpose of brevity here.

Life is something for which we can readily define almost universally accepted necessary criteria for, but struggle with creating sufficient criteria. It’s clear (at least, to me, and to the vast majority of recognized experts) that computers and/or the software they run are not alive, even though they can very well be programmed to meet necessary criteria. The “gray zone” that you consider straddles that region of categorization. However, viruses clearly fall below the “necessary” line; while demonstrating a few of the characteristics of what is recognized as being alive, they fail to demonstrate some of the implicit qualities we expect in anything living; specifically, the ability to autonomously consume or replicate. You can redefine life to encompass the “behavior” of viruses, but this is an excursion well and truly away from any definition of living. Although you continue to describe this as an arbitrary distinction, it in fact derives from the very core of what living organisms do; they self-replicate, preserving their form for “future generations”. While it’s true–and thermodynamically necessary–that they draw energy and nutrients from their environment, living organisms universally take responsibility for the process of replication themselves, even those whose livelyhood is parasitically dependent upon another. Viruses, on the other hand, are helpless to do anything outside the confines of a living cell; they have no capability for respiration, much less reproduction. We don’t even regard mitochondria or choroplasts–which are vital to the intracellular metabolic processes–as alive outside the cell even though they were once almost certainly independent organisms. This has nothing to do with “pleasing” scientists than identifying unique, fundamental principles which underlie the nature of life.

The analogy to planets and in particular Pluto is misapplied (as is any analogy when stretched too far); I would certainly agree that the classification of objects orbiting a star into “planets”, “dwarf planets”, and “asteroids” is largely arbitrary. Planets and stellar systems are not self-propagating systems, though; not only do they follow strict mechanical laws, but they cannot be classified as a self-regulatiung thermodynamic system. Esssentially all the internal energy that a planetary system has comes from its initial angular momentum and the amount in which this changes over time is virtually insignificant. On any reasonable timescale planetary systems are in equilibrium. On the other hand, biological systems are dramatically non-equillibrium systems–they see rapid changes in energy throughput–and by any reasonable standard we’d expect them to come apart like a cheap gold watch, whereas systems described as “living” manage to organize and regulate the flow of energy, actually contributing to their internal organization albeit while still producing a net entropy for the overall system. Note that even this is not a “sufficient” criteria for life (systems that are clearly non-living, like geysers and mechanical steam cycles can also demonstrate regulatory behavior) but is a necessary one.

Regarding self-regulating and cellular structure in nature, cellular organization can be found in virtually any ongoing thermodynamic system with defined boundaries, from the granules in the Sun’s photosphere to convection cells in both the Earth’s mantle and atmoshpere, to Bernard-Rayleigh cells and spiral Taylor flow inbetween rotating cylinders. When I suggest that live of any kind would almost certainly develop along cellular lines, it’s not out of what you describe as “one person with rigid views” based on the single data popluation of terrestrial life, but that cellular organization of some form is implicitly necessary in large scale organization required for a self-replicating structure. We’d no more expect that a living organism would exist as a gestalt without divisions than that a computer program could be stored in a single, massive ferrite core. This isn’t to say that extraterrestrial life will in any way resemble the overall form or structure of life as we know it–indeed, while we have good reasons to believe that life based upon carbon macromolecules is significantly more likely than alternatives based upon silicon or other structural polymers–but it will almost certainly have a cellular organization and division of labor, based upon the necessity of evolving from simple processes which form the basis for more complex steps. You can pitch this aside as rigid and uncreative thinking if you like, but I challenge you to propose a credible alterative which is not organized in simple units compounded together to form more complex structures.

Stranger

[Stranger_On_A_Train]

[QUOTE=Darwin’s Finch]
The problem being that it requires an inaccurate metaphor to explain genic selection as a universal phenomenon; you practically have to consider genes to be alive (to bring this thread full circle), or at least treat them as if they were, in order for the metaphor to make any sense at all. Actual examples of “selfish genes” can be found, and described, without resorting to metaphor at all.
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It’s necessary (or at least convenient) to resort to metaphor to describe it in plain discourse, but, at least for simple scenerios, it’s possible to model the “selfish” behavior of genes as a game theory problem and find an equilibrium solution. Gene-centric theory is hardly alone in this; it seems impossible to explain quantum mechanics to a general audience without talking of particles “seeing each other” “collapsing”, et cetera even though there is, from the strict mechanics of it, no reason to believe that any volition on the part of anything involved (certainly not electrons) is responsible for the result of an interaction. For any complex genetic scenerio, the number of interactions and attendant complexity is such that creating a useful prediction (notwithstanding non-genetic behavior), without gross simplification, is essentially impossible, at least for now. On that basis it would be reasonable to argue that even if it had merit, it’s practically useless as a working theory, but as an underlying, unifying mechanic I find it much more satisfying and workable than higher order selection. One can argue that in, say, kin selection, the frequency of shared alleles dictates the degree to which altruistic behavior is demonstrated, but it fails–at least in my mind, and again I’ll freely admit to lacking a comprehensive academic grouding in the subject–to explain “why?” an organism would sacrifice itself for its kin. So what if they share a common allele; save for human beings, no creature is explicitly aware of this, and arguments for implicit, instinctual behavior for apparently altruistic sacrifice based upon shared genes without resorting to the common “interests” of the genes themselves still leaves me grasping for something which links the sacrifice behavior to the gene.

[QUOTE=Darwin’s Finch]
As such, I see genic selection as a tool, rather than the whole toolbox. I also see, as you may have noted, genic selection is a distinct form of selection from natural selection (possibly a reversal from some previous posts I’ve made here – I don’t recall how I’ve phrased it in the past – but I’ve been thinking upon this a bit more of late).
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I’m not at all clear how or by what you mean that genic selection is distince from natural selection. It’s true that the selective pressures act upon the organism in which the gene resides and expresses itself via the phenotype, so there is a certain proxy relationship (i.e. gene–>phenotype–>organism) but ultimately the success or failure of a gene in general form depends on the benefit or detrement it provides to the resulting organism as a result of its phenotypical expression. While this adds a layer of abstraction, I’m afraid I don’t see how this is not precisely natural selection in the same way that an pack predator’s success is predicated on not only how effective of an individual hunter it is but on how well it contributes to the group. It seems to me–perhaps in my admitted ignorance–that while viewing selective pressures as occuring in higher level divisions is useful in terms of emperically qualifying the effect upon resultant evolutionary developments, such high level mechanics fail to converge to a more general explanation, resulting in what are in my view unnatural distinctions between kin selection, group selection, and organism selection.

Stranger