Tuesday, January 20, 2009

Even more pits

OK this is the latest in an ongoing conversation I'm having with Johnny on the issue of pits, the first two installments can be found on his blog Johnny provided some comments on my previous pit post and I have brought them up to the front to answer them. Johnny's comments are blockquoted.

Since we agree that Mt. Improbable is a good analogy for its intended purpose, I’ll move on.
Um, hang on. I say that Mt Improbable is ok as far as it goes. The problem is that it doesn’t go very far! The analogy doesn’t cover all evolutionary processes, only adaptation. There is no climbing involved, and evolution is directionless, it doesn’t proceed upwards. So, apart from that, yeah, it’s OK.

Viewing the two blog post here, as well as the two comments you were kind enough to provide to the “rebuttals” at my site, I think that, broadly speaking, there are a couple of assumptions or implications being made that are fundamentally false – false, based on my understanding.

1. You describe Natural Selection as acquiring beneficial alleles through a “random process.” This is incorrect; NS is a non-random cumulative process.
The generation of alleles is random, the concentration of them may or may not be. The concentration of beneficial alleles is non random, but “non-beneficial” alleles can also be fixed.

2. You imply that genetic drift contributes to fitness when, in fact, drift is a random process that is entirely disconnected from fitness. (Big point)
Actually I didn’t mean to imply that GD contributes to fitness. It may do, if the fixed alleles subsequently provide the starting materials for beneficial alleles, but at the time, no, there is no increase in fitness.

3. Through descriptions of lateral jumps between peaks, distances between pits and by suggesting that new “groups” can arise by “breaking through new fitness landscapes,” you’re implying that a Genus, Class or Family can erupt from a Species. This is false. Species rise from “speciation” at the species level. There is no jumping between points – only steps - a continuous gradation.
I’m a bit confused here. Genera, Classes and Families, while artificial constructs, are formed initially from one species – the common ancestor of the group. The original population undergoes a concentration of alleles into a pit which sags If that concentration of alleles becomes intense enough, ‘bottom’ of the pit separates from the original population’s topography, producing a new species (if there is no link then there can be no allele transfer = genetic isolation and so a new species.) We now have two species, represented by the original topography, and the new topography, species 2, which is orbiting close by. Say the original species undergoes another speciation event to produce species 3. Now we have three species cluster closely together in morphospace, as they share more alleles in common with each other than they do with any other species.

This grouping of the common ancestral species and its descendant species would comprise a genus, but with the caveat that the boundaries of which species would be classed as in the genus or outside is an arbitrary one. Speciation still occurs over time, with no major jumps.

4. You imply that “Generalist” and “Specialist” are definitive forms by saying that one has survival value over the other. These are relative terms. You may view/classify a particular insectivorous mammal as a specialist because its diet is limited to only insects – I could counter by saying that it’s a generalist because it eats a wide variety of insects as oppose to limiting its consumption to termites. Without knowing the type and extent of a theoretical catastrophe – there is absolutely no way to predict what niches will remain intact or the rate to which any event survivors will rebound.
There is no doubt that specialists can be very successful, and you are right that there is no telling which niches will survive. But specialists with adaptations to a specific environment may well be at a disadvantage should the environment shift and close out the niches to which it has become adapted. Under those circumstances the species is carrying a load of alleles that are no longer useful. If those alleles produce adaptations that have a high production and maintenance cost, then they are disadvantaged compared with other species which, while not dominant in the previous environment, do not carry the extra load and so may be in a better position to survive.

On an individual species basis significant adaptation may well provide dominance in a certain niche, but that species is more likely to disappear if the environment changes compared with other species that are more general and hence can survive in a number of environments. Generalists generally do not dominate any niche, but exist in several. Specialists dominate in one niche.

5. You create a false dichotomy between peaks and pits; both are landscapes and as the term “landscape” suggests, both represent a varied ever changing state complete with valleys, ridges, prairies, bumps, holes – they are one in the same –metaphors for change.
Yes, but as I mentioned above the Mt Improbable analogy doesn’t cover all evolutionary processes, only adaptation. There is no climbing involved, and evolution is directionless, it doesn’t proceed upwards.

6. You imply that organisms adapt or imbed themselves into a static environment, when in fact static environments don’t exist. Ecology is a balancing act, therefore so is adaptation.
The environment is not static, and adaptation works to balance this, but become too specialised, and have the environment shift too much, and the species is left high and dry.

7. When comparing short-term success with long-term survival you seem to suggest that evolution is a fundamentally different process following some catastrophe or major ecological shift. This isn’t so; the same processes driving speciation, drift and natural selection today are the very same processes that will drive evolution following an asteroid impact. If adaptation and specialization are what is successful in the here-and-now, they are also going to be successful strategies following a catastrophe.
Actually, evolutionary processes are the same, it’s just that after a major ecological shift it is more like to be generalists that repopulate first and become the source of new species (yes, by adaptation).

8. Describing both Natural Selection and Drift in terms of allele frequency is fine; however keep in mind that NS works with phenotypes as well as genotypes; this builds the link to fitness. Drift does not have this link.
Yes Natural Selection works well, there’s no argument there. But NS isn’t the only process at work, and the Mt Improbable analogy only covers adaptation. A description that covers all evolutionary processes would be better.

9. The idea that a current level of adaptation exhibited by an organism somehow reflects its future potential or its available genetic plasticity is erroneous.
OK, what if we have two organisms. A with small feet adapted to dry ground and B with larger feet. A is dominant in the environment, but B is OK on dry ground, but can also access marshy ground. Now, suppose the environment changes to all marshy ground. Can we say nothing about the future potential of these two organisms?

However, I do admit, the visual image of a “sag” being created by the weight of an area with increased allele concentration is pretty catchy…
Yeah, one does tend to gravitate towards it . . .

1 comment:

  1. Ugh, I was hoping that the “since we agree…” statement would slip by unnoticed…

    1. I wasn’t very clear here. I intended “beneficial alleles” in the same sense that you mean “concentration of beneficial.” As something more than just a random mutation; as something selected. Neutral, or “non-beneficial” alleles are not fixed through NS because they would lack a beneficial phenotype – NS requires phenotypic advantage.

    2. Implying that Drift may lead to improved fitness at some point down the road is equitable to predicting exaptation, which in turn is the equivalent of predicting future ecologies. Exaptations are visible in hindsight only and are far too infrequent to be a major evolutionary driver.

    3. Absolutely. If you didn’t intend the mention of groups breaking through new fitness landscapes as something other than a graded change at the species level, we are in agreement. Yes, classification systems are constructs - that was my intended point.

    4. Sub-Point A: The terms are still relative; give me an example of an extant generalist and I’ll point out why it could be considered a specialist. Rats & raccoons, cockroaches & crocodilians – all highly specialized.
    Sub-Point B: I’m failing to grasp the idea of burdensome allele loads… By any measure Pakicetus would have had an enormous “allele load” during its trek to towards whale-hood; however, I wouldn’t say that it was burdened or at a disadvantage – quite the opposite.

    5. You’re comparing Apples and oranges, or more correctly apples and apple seeds. Evolution isn’t progressive – adaptation is “progressive” in the broad sense that phenotypes are selected based on a value system of ecological fit; adaptation is a non-random component of evolution.

    6. To make this claim, I feel, requires delineation of both the level of specialization and the amount of ecological shift to which you’re referring. There are too many variables to define a rule.

    7. A catastrophic incident (e.g. asteroid impact, etc…) is not an evolutionary process, it’s a physical event. So, suggesting that the extinction of specialists as a result of such an occurrence is indicative of long term evolutionary success is a non sequitur.

    8. If it can be achieved in a clear, meaningful and memorable way… The current debate.

    9. I think that the deck may be stacked with an exaptation in this example, unless you’re trying to make my point that better adapted organisms exhibit greater fitness… But yes, we could say that both A and B, if constrained to the same environment, would move towards better adaptation to that environment. I don’t think that either would be considered a generalist (they’ve adapted to their current ecology), nor do I think we could predict which would survive a sudden flood (catastrophe). Further, I don’t think we could say that if a prairie undergoes transition to a marsh that the organism with small feet will go extinct or is at an “evolutionary cul-de-sac”.

    Maybe my internal visualizations of the pit model are in error??? Do you think that you could put together a sketch (an animation would be great, though certainly more involved!)?

    Thanks - good stuff.


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