MrDarwin

Here's your problem right here. We aren't. Populations of animals are separated by geography and habitat. Animals that live in different habitats don't generally compete with each other. There are different selective pressures on these different populations. Ecological niches are influenced by geography, altitude, temperature, vegetation, availability of water, as well of degree of seasonal variation in temperature, day length, precipitation, etc. Such habitat variation has existed on the earth since life first appeared.

The processes that drive evolution include such wild cards as mutation, habitat change, and unusual events like volcanic eruptions and asteroid impacts.

Maybe in a stable, unchanging environment. In other words, not in the real world. The flaw in this argument is in the underlying premises.

See above. In a nutshell, variation in climate, environment, and habitat, both geographically and over time, prevent this.

Duvenoy

Evolution has neither goal nor direction. It is not trying to develop the ‘perfect’ animal, whatever the species. It is simply trying to adapt the animal to it’s environment using whatever parts that happen to be laying around the shop - that is, the animal it’s self. The result has turned out some very odd creatures, the previous example of echinoderms being an excellent one (I caught that show and wish I‘d taped it so I could see it again). We, ourselves could be considered another. But we have a long way to go before we catch up with the sea star and the sea urchin as far as species success and longevity are concerned.

Some time back, I was on the periphery of a less than heated debate concerning human evolution. The subject was: “Has human evolution come to a stand still?” There were some pretty good arguments saying that we are no longer evolving. One was to the effect that we are quick to treat diseases and have artificially taken all predatory pressure off our species (with the exception of ourselves). Also, we no longer have to forage for food and we easily shelter ourselves from the elements. Therefore, we have ceased to evolve because there is no longer a reason to do so.

Yeah but, the opposing argument went, no one has ever seen evolution at work. All we have ever seen are the results of it. Therefore, you cannot say that we are not evolving. We are certainly evolving but our evolution is being directed by pressures in our self-made environment that are different from those of our savanna-roaming, hunter/gatherer/scavenger ancestors.

I myself, tend to favor the second argument.

Here’s a splendid example of parallel evolution: I keep a fascinating serpent called a, “Rinkhal’s Spitting Cobra (Hemachatus heamachatus).” This snake looks like a cobra, hoods and hisses like a cobra, has ridged fangs and spits venom from them for all the world like many cobras. But it is only related to cobras (Naja) in that it is an Elapid.

A close look at Hemachatus (it’s the only species in the genera) will reveal that it has heavily keeled scales. It also gives birth to live young. It is unique within it’s family. But damn, don’t it look and act (and bite) just like a cobra?!

Oh yes, and when panicked, Hemachatus will play dead better than any opossum, a most un-cobra-like action. Amazing animal! Evolution rocks!

So, there’s few thoughts on the subject.

luck,

d

theyeti

When intra-specific (within species) competition becomes greater than inter-specfic (between species) competition, then two species will coexist. This helps to drive specialization among many species. Basic ecology.

theyeti

theyeti

This does not at all mean that the introns are doing something. Most likely, it's a problem with the expression system. Not all eukaryotic genes can be expressed in prokaryotic systems. Has anyone tried expressing the cDNA in a eukaryotic system? And what does this have to do with the abundance of genes that express fine without introns? Do you think that one single counter-example demonstrates that they all have a function?

BTW, I don't see how you figure that the appendix is "important". How do so many people get by with no ill effects when this "important" organ is removed?

theyeti

Yellow3

People get by fine when the spleen is removed as well. Same as with the tonsils. And yet neither of these organs are unimportant or have no function; it just means that we can get by without them, often because other organs or lymphoid regions in the body can take up their function if need be (the liver takes up blood filtration for the missing spleen, other lymph nodes make up for those removed). The appendix serves the same function as any other region with large aggregations of lymphoid nodules, e.g., the noninvoluted regions of the thymus, the lymphoid nodules, Peyer's patches of the ileum, et al. It's part of the lymphoid system and thus does do something, and probably when it is gone the slack is taken up by the other lymphoid nodules of the lower gut. Just because it's also prone to blockage and infection does not mean it doesn't do anything. It just means it's poorly designed (if you can call it that), like the human prostate.

And as for the intron thing, I will cede that one since the only way I know about it is because my friend was describing the migraines she was having with it (must learn to mark hearsay vs. stuff out of my textbooks and articles as such next time I post). I think they were trying to figure out how to get the thing to work for gene therapy (so it was being expressed in a eukaryotic cell at the end), but the only way to get it into the viral vector was to take out the introns. Insert into host cell and bingo - nothing (I would guess something got screwed up in the posttranscriptional splicing and signalling due to no introns, myself). And incidentally, when was I saying they all have a function? The original statement was that introns have no function whatsoever, ever. If the problem with these blood clotting factor introns is something in the intron necessary for production of proper proteins, then introns are not simply "junk DNA" through and through, although one being useful does not necessarily mean that all of them actually do something.

- Jen

[ May 13, 2002: Message edited by: Yellow3 ]</p>

theyeti

Okay, fair enough. I think it's worth noting that the tonsils and appendix (don't know much about the spleen) have a bad tendancy to get infected and inflamed and are potentially deadly to you. They are clearly good examples of vestigal organs. Remember that vestigal does not mean that the organ in question does nothing, only that it's become redundant, obsolete, or greatly diminished from its original state. We would be better off without an appendix.

Right. Gene therapy by its nature is difficult and prone to causing migraines. As for alternative splicing, that should be already known from studies of the wild-type gene in vivo and northren blotting. Either way, you should still get expression, just not of the transcript you want.

One thing is for sure, and that's that introns help facilitate alternative splicing, which may be one reason why they evolved (or at least why they are maintained). They also promote exon-shuffling, which allows for the creation of novel new genes. However, in either case the internal sequence of the intron is irrelevant (with the exception of a tiny bit of spliceosomal sequence). What matters is merely the intron's structural presence, so thus when you said this...

...you were wrong to exclude introns. Introns, even if they have a structural function, are still neutral with respect to their internal sequences, and thus are widely used for studying mutation rates and drift. In fact, intronic sequence divergence is frequently used in comparison with exonic divergence to estimate the rate of adaptive evolution. When the exons diverge faster than the introns, you've got positive selection; slower, stabilizing selection; the same, drift.

I don't suppose you did, but when you made the statement...

...you were making a generalization. I don't think this is a generalization which holds, at least not in the case of introns. In fact, I would contend that the generalization is strongly favored for the opposite case.

Since when did I or anyone else make that statement? Molecular biologists originally found introns to be puzzling, and bent over backwards to find a purpose for them, but none seemed to be forthcomming. Then Walter Gilbert explained them in evolutionary terms, and made many predictions that have since been borne out. One thing he predicted is alternative splicing, which is a structural function of intronic sequences. However, it was realized that the sequence itself is not important in this regard, and can thus be properly thought of as "junk" (incidentally, I don't like the term "junk" because forces us to ignore the origins of a sequence; introns are almost certainly derived ultimately from transposons, whose sequences cannot be regarded as "junk", but have since had everything but their splicing ability become "noise"). In fact, introns can differ greatly in the length and sequence between related organisms, even though the intron/exon structure is in most cases identical.

Again, I think you're generalizing. If this particular blood-clotting factor needs its introns, then it is a very peculiar exception, not a rule. It would mean either that this particular protein aquired a dependence on them, or that all others have since lost their dependence on them. Either way, 99% of introns are "junk DNA" through and through.

theyeti

P.S. Sorry about being argumentative, but ARN's been down for some time.

Yellow3

I'm gonna let the intron/exon thing go, since past what I've said already, I don't really have the expertise to go argue this stuff - I muddled through genetics and biotech, but knowing what these things are and (generally) how they are spliced doesn't necessarily mean I can tell you what the hell it's all for. (hell, half the time I can't remember what the chemical I'm using at this moment is for)

However:

Ah. I think generally 'vestigial' gets thrown about in terms of 'obsolete' and there's the confusion. The appendix is not obsolete, although we can and often do live without it, and we don't depend on it for much like do certain herbivores like the horse and the rabbit for digestive functions. All the things it has that make it an important immunological site (the lymphoid nodules, the M cells, the paneth cells) are present at other regions of the gut, and these other regions can do the work if the appendix goes missing. Would we be better off without an appendix? We'd probably be better off with one less prone to blockage, that's for sure.

As for the tonsils, well, I can't really say much about them because we had to skip over them for time in histology. I know their primary function is response to airborne and ingested pathogens, but we can live without them, so as far as I know they're not vital like true lymph nodes are. Would we be better off without them too? What was their original state that they're diminished from, or do they have one? Do people that have them removed experience any effects to the efficiacy of their immune system, even slightly? I have no flipping clue (although I'll tell you, just skimming over the readings for tonsils, the palantine ones at least are pretty damn gross).

And - eh, don't worry about the argumentative bit. I'm kind of running on the short side of temper myself due to sleep deprivation and stress, it being finals time on my end, so I should probably be good and wait until I'm a little less high-strung to post more. Although I do remember my histology teacher harping again and again in lecture about the appendix not being a vestigial organ anymore because it's part of an active system (lymphoid organ). . . but I think I'll bug her about it after the final. Don't want to explain what I'm doing goofing off right now instead of squinting at slides of seminiferous tubules.

What's ARN, anyway?

- Jen

Lizard

I think some of the confusion about "competition" has to do with a misunderstanding of Darwin's basic concept. I believe he was talking about competition for resources among members of the same species. It is via intraspecies competition that advantages conferred to individuals by genetic mutation are naturally selected for. The animal that has a slight genetic edge over its fellows in the hunting department gets more food, reproduces more, and gets more of its genes into the pool. It is my understanding that interspecies competition is far less common and produces far less variation than does the intraspecies kind.

MrDarwin

This article may be of interest here, as it specifically addresses why ecosystems are not stable over time:
<a href="http://www.sciencedaily.com/releases/2002/05/020514072408.htm" target="_blank">Ocean Ecosystems Only Altered Following Two Great Mass Extinctions; Unexpectedly Stable Over Hundreds Of Millions Of Years</a>

[ May 14, 2002: Message edited by: MrDarwin ]</p>

Skydancer

Wisdom teeth may be relict structures. They're quite useful if you have a diet high in abrasives - they'll replace your secondary molars as they wear out. Since this doesn't happen to Westerners much any more, they try to grow into a non-vacated space and cause trouble.