Use brain much

[Lupernikes_shadowbark]

but i'm not a biologist....i was being ironic only.....not seriously scientific

[Kai]

but i'm not a biologist....i was being ironic only.....not seriously scientific

Its ooooooooooooooooooooooold.

And overdone. Please, I hear enough from creationists to make it so completely unfunny.

I also claim all right to abuse people for annoying me about this stuff, wallow in my mistakes and apologize for it later (if necessary).

[Cain]

[Dr Goofy]

I left my wip at her house.... damn it!

[Elder Iptuous]

Perhaps this is what is confusing me....
Do use "evolve" : incorrect connotations but commonly used and understood, except by those that don't understand (fuckem)
however
Do never use "de-evolve" : incorrect but commonly used and understood, except by those that don't understand (fuckem)
Insist on "return to more ancestral body plan" : correct but not commonly used or convenient enough to ever likely gain common use.

Not trying to be confrontational, I'm just trying to appeal to your authority as a biology guy to understand the motivation behind the terminology.  Is there a movement in the biology field to replace the term 'evolution' because it has deeply ingrained connotations of progress towards some ultimate goal?

Also, can you point me at good reading material on debate over whether evolution is in fact progressing towards a goal? (perhaps of greater ability to live and reproduce in wider array of environments)

Thx

[Kai]

Perhaps this is what is confusing me....
Do use "evolve" : incorrect connotations but commonly used and understood, except by those that don't understand (fuckem)
however
Do never use "de-evolve" : incorrect but commonly used and understood, except by those that don't understand (fuckem)
Insist on "return to more ancestral body plan" : correct but not commonly used or convenient enough to ever likely gain common use.

Not trying to be confrontational, I'm just trying to appeal to your authority as a biology guy to understand the motivation behind the terminology.  Is there a movement in the biology field to replace the term 'evolution' because it has deeply ingrained connotations of progress towards some ultimate goal?

Also, can you point me at good reading material on debate over whether evolution is in fact progressing towards a goal? (perhaps of greater ability to live and reproduce in wider array of environments)

Thx

Charles Darwin in his original draft of On the Origin of Species did not use the term evolution. Neither did he use the term "Survival of the Fittest". He actually dislikes both these terms very much. They were coined by his contemporary Henry Spencer, and he did not include them in his book until the 5th reprinting. They had become so popular with the public that he was more or less forced to adopt them with respect to his hypothesis. The reason he didn't like the terms is because, while he did observe an increase in complexity over geological time, he did not see this unrolling (which is the literal meaning of evolution) of species, which suggests progress, and in the public eye, progress towards perfection, some goal, utopia, etc. He saw lineages become extinct as often as he saw them making it.

Modern science tries to stay with this early understanding of the mechanics of what is now called evolution, but is really an adaptation of Darwin's modification with descent. To see some sort of inherent progress in biology is a very human bias, as we have a tendency to see progressions in nearly any medium. Thats how we think. To combat this bias, biologists refrain from using phrases such as more evolved or less evolved. Instead, we talk of phylogeny, the origin of lineages, and of particular species or groups being basal or derived in characters with relation to their common ancestors. This removes the human bias of progress, and allows us to see the processes much more clearly.

For example (one that I gave in another thread) the evolution (in the context of descent with modification) of wings in the insect order Phasmodea. Humans tend to see wings as progress and "more evolved", so before genetic evidence they grouped the winged walking sticks and the unwinged walking sticks separatly, with the winged ones "more evolved" and the unwinged ones "less evolved". As it turned out though, wings in walking sticks have been "lost and found" again in several lineages, due to an "on off switch" for the genetic sequence for wing development. This does not denote any sort of progress, no less than mammals returning to the oceans in the form of whales and dolphins show any sort of upward movement. The goal of life is "whatever works", and the species are here today are simply the lineages that have made it, while 99% of all other species that have ever lived have been lost.

In conclusion, yes, that is the connotation, and yes, biologists, or the ones who aren't all political about it, tend to be very specific with terms in order to remove that bias of progress.

As far as reading, I can't think of anything off the top of my head. We already have organisms that can survive extreme environments, we have tardigrades that can survive cryptobiotically in outer space for a time, we have bacteria and other organisms that live in extreme cold and extreme heat, we have deep thermal vent organisms that are chemosynthetic, completely cut off from the sun, there are aquatic organisms in deserts that can survive long periods of dessication, or in the artic and antartic, frozen conditions.

Actually, there have been a bunch of books written on extremophiles. What you are talking about are unfilled niches in environments. Niches empty and fill all the time, its actually a rather essential part of the modification of lineages; open resources are quickly acquiesced, cladogenesis occurs all over the place because of it. Life pretty much covers the planet, there are very few niches which have not been filled on a large scale since the invasion of land in the early Paleozoic.

Thanks for listening.

[East Coast Hustle]

damn.

that's the most interesting thing I've read today, at least.

[Elder Iptuous]

Good response. thanks for taking the time.
You have mentioned that it is simply human nature to think of the process as a sort of progress even though it isn't.  You may very well be correct, but I'm having a hard time giving up on that idea, too.  (Again, not trying to simply be belligerent or closed minded)
Considering the notion of an 'ultimate form' that an organism might  progress towards, a  superficially obvious definition that occurs to me would be one that allows the creature to live and reproduce in any environment that might befall it.  You mentioned the extremophiles that we have cataloged but are these organisms able to exist in a broad range?  I guess the examples that pop into my mind are the sea vent creatures at very high temps.  I don't know, but i'm guessing they are not able to exist at temperatures much beyond that niche that they are in.  Would it not be 'progress' if they could withstand these temps and lower ones?  This would likely involve more complexity, though, right?  Would it be innacurate to say that there has been an increase in complexity of organisms over time?  And would this indicate that the higher levels of complexity are advantageous over a broader range of environment?
You mentioned the genetic switch that controls the wingedness of that insect.  I find that very interesting that a fully functional and complex feature can be coded in the genetic sequence of an organism with only a gene or two that allows/causes it to be expressed.  If a creature had a highly complicated genetic repetiore of features like this that allowed it to very quickly adapt to changing environments, it would seem reaaaaly hard for me to not think of it as 'more advanced' that a creature that didn't, and would be unable to adapt as quickly to a changing environment...

[Golden Applesauce]

Good response. thanks for taking the time.

You have mentioned that it is simply human nature to think of the process as a sort of progress even though it isn't.  You may very well be correct, but I'm having a hard time giving up on that idea, too.  (Again, not trying to simply be belligerent or closed minded)

Considering the notion of an 'ultimate form' that an organism might  progress towards, a  superficially obvious definition that occurs to me would be one that allows the creature to live and reproduce in any environment that might befall it.  You mentioned the extremophiles that we have cataloged but are these organisms able to exist in a broad range?  I guess the examples that pop into my mind are the sea vent creatures at very high temps.  I don't know, but i'm guessing they are not able to exist at temperatures much beyond that niche that they are in.  Would it not be 'progress' if they could withstand these temps and lower ones?  This would likely involve more complexity, though, right?  Would it be innacurate to say that there has been an increase in complexity of organisms over time?  And would this indicate that the higher levels of complexity are advantageous over a broader range of environment?

You mentioned the genetic switch that controls the wingedness of that insect.  I find that very interesting that a fully functional and complex feature can be coded in the genetic sequence of an organism with only a gene or two that allows/causes it to be expressed.  If a creature had a highly complicated genetic repetiore of features like this that allowed it to very quickly adapt to changing environments, it would seem reaaaaly hard for me to not think of it as 'more advanced' that a creature that didn't, and would be unable to adapt as quickly to a changing environment...

The 'genetic switch' is really quite simple.  Protein-coding genes have to be 'read' by other molecules before they can be expressed as a protein.  (Developmental biology is still working out how little bitty proteins get complicated structures to organize.  But we know that they do.)  All you have to do to switch off a feature, then, is to code for a protein that latches on to the DNA of another gene, thereby preventing that gene from being read.  Think of it like putting a wad of gum on a record - no matter how complex the music, a simple little wad of gum will prevent it from playing correctly.  (This is a little bit of an oversimplification.  There are lots of other ways that genes are regulated, and the proteins that they produce can also be regulated.  There are even genes that can code for totally different proteins in different circumstances!)

Now, about your idea of progress meaning being broadly adapted.  That is certainly a way for an organism to be more viable, especially against habitat loss.  But you'll find that specialization increases efficiency.  The ocean vent dwelling extremophiles, for example, are anaerobic, meaning that they do not require O2 to keep their metabolisms going - in fact, I believe that O2 is toxic to them.  Most organism are aerobic, at least, they are after the Earth's atmosphere became 20% O2.  An organism that had one metabolic pathway that used oxygen and another that could function without oxygen would have an advantage in the greater range of habitats it could live it - but it takes more energy to keep two totally different metabolisms going.  So in oxygen, the aerobic organisms would have an advantage by not having to lug the dead wait of an entire energy system that is non-functional around O2, and anaerobic organisms for the same reason without oxygen.  Therefore, evolution favors speciation into two organisms, each to its own niche, as the best competitors.

Think of it this way: you're carrying around survival gear for every possible environment, while I am merely specialized for say, the desert we're in.  (I've reread Dune recently.)  We've both got moisture conserving tricks and ways to beat the heat in the day and the freezing temperatures at night.  You, however, are also lugging around a bulletproof vest, a spacesuit, a SCUBA mask, a snowsuit, and forest camo gear.  Guess who can get food while expending the least amount of energy?  Me, which means in the long run I'll have more energy to devote to my offspring.  Sure, you can handle outer space - but we're not in space.  So I win. 

Now as for your idea about having a super-adaptable toolkit-like DNA, remember that mutations are random.  So if your organism could easily adapt by recovering its ancestral wings when those would be a net plus, it would be just as likely for it to recover its ancestral wings when they would do more harm than good.

About organism becoming more complex over time... sorta.  Cells with mitochondria are more 'complicated' than cells without mitochondria, and they ded came later.  Multicellular organisms did come after single-celled organisms, and came before organisms with organs.  But then again viruses came after cellular life.

ETA: Kai, I think it's pretty amazing that we have member dedicated to bringing us science news, identifying our insects, and explaining biology terminology.  Keep it up!

[Golden Applesauce]

Also, can you point me at good reading material on debate over whether evolution is in fact progressing towards

The idea of directed evolution is quite popular among the Intelligent Design crowd.

[Kai]

Good response. thanks for taking the time.
You have mentioned that it is simply human nature to think of the process as a sort of progress even though it isn't.  You may very well be correct, but I'm having a hard time giving up on that idea, too.  (Again, not trying to simply be belligerent or closed minded)
Considering the notion of an 'ultimate form' that an organism might  progress towards, a  superficially obvious definition that occurs to me would be one that allows the creature to live and reproduce in any environment that might befall it.  You mentioned the extremophiles that we have cataloged but are these organisms able to exist in a broad range?  I guess the examples that pop into my mind are the sea vent creatures at very high temps.  I don't know, but i'm guessing they are not able to exist at temperatures much beyond that niche that they are in.  Would it not be 'progress' if they could withstand these temps and lower ones?  This would likely involve more complexity, though, right?  Would it be innacurate to say that there has been an increase in complexity of organisms over time?  And would this indicate that the higher levels of complexity are advantageous over a broader range of environment?
You mentioned the genetic switch that controls the wingedness of that insect.  I find that very interesting that a fully functional and complex feature can be coded in the genetic sequence of an organism with only a gene or two that allows/causes it to be expressed.  If a creature had a highly complicated genetic repetiore of features like this that allowed it to very quickly adapt to changing environments, it would seem reaaaaly hard for me to not think of it as 'more advanced' that a creature that didn't, and would be unable to adapt as quickly to a changing environment...

Well, there are generalists and specialists. Now, I'm not sure this is true, but when there is a great deal of environmental change, the generalist will win out, but when change is much slower, the specialists will easily be more successful in their actualized niches, because they can take full advantage of the resources therin, whereas a generalist can only take partial advantage. Compare norway rats and beavers. Both are very successful within their range, one is an extreme generalist, the other is a relatively good example of a specialist. The norway rat is able to take advantage of a wide variety of environs, but is unable to access all the resources of any single niche they might fill in any environment. The beaver, on the other hand, selects for poplar lined streams, builds a dam and creates an artifical lake, and feeds on the poplar, their prefered food source. This is a much more specialized animal, it requires a specific habitat, but it can take much more advantage of the resources in that single habitat than the norway rat would be able to in any single habitat.

Makes sense? This is why we have generalists and specialists. There are temperature generalists, but because they have a wide range of temperature tolerance they can't specialize and survive very extremes of hot and cold. Then there are temperature specialists, like the hot thermal vent bacteria, or hot spring organisms, or amphibians from the arctic circle that can stand frozen conditions, but they can't live much where else.

Ecology abhors an organism that is 'perfect', in the human sense of able to access all environments and all resources. The reason for this is generally because such an organism would cause an ecological catastrophy, eventually leading to the breakdown of the whole system, and the extinction of that organism. About the only example I can think of is Homo sapiens sapiens, and its only through technological means that we are able to survive in some of these environments, and not well. We still cannot access all resources of any environment. We can't digest cellulose, we can't survive temperature extremes, we can't survive in aquatic habitat, or saline. We are terrestrial ominvorous generalists with large brains and tool making capacities beyond other organisms on this planet, but that does not by any means dictate we are better than all the rest. We /think/ we are, but I suppose any species with a cognitive sense thinks they are the best.

Now, complexity. This has always been a rather debated topic. Complexity is usually refering to forms that are more derived from their basal ansestral counterparts. But we see systems simplify as often as they complexify. We see diverse lineages being lost /more often/ than we see them being retained.

The Burgess shale is a good example of this. Its a fossil bed in British Columbia that dates back to the Cambrian period, 540 mya or therabouts. Just /prior/ to the Cambrian period, about 570 mya, there was a great diversification of life over about a 10 million year arch, where almost all modern phyla of life arose. This is usually termed the Cambrian explosion, which is a misnomer, since it took place in the Precambrian and over a ten million year period, not really all that explosive if you ask me (The Cambrian explosion was neither Cambrian nor an explosion. DISCUSS.) Anyway, back to the Burgess Shale. In this fossil formation, we find a massive variety of body plans, many of which are not seen today, things like half arthropod, half fish, or weird worms with jointed appendages. All of these organisms did not continue their lineages past the Cambrian period. Only a few select body plans were successful afterwards, and the rest were lost. Diversification led to simplification, leads to diversification leads to more simplification. In fact, we could say that generalists are not more complex but more simplified than their specialist counterparts, they have a more general body plan, more general, less specialized behavior. You find more system complexity in specialized habitats, where complex behavior and biology are needed to take full advantage of the resources. And diversification and simplification cycles like this, in species, in lineages, in phyla.

GA: the gum on the record is the best metaphor I have heard for the gene switches. If I remember right, it has something to do with the unrolling and reroling of the DNA molecule so that some areas are all bunched up tightly and can't be accessed and other are more loose and linear, allowing DNA Helicase to work correctly, and then there are enzymes that can roll and unroll the helix. Its been years since I've had genetics, am I even close?

[Kai]

Now, about your idea of progress meaning being broadly adapted.  That is certainly a way for an organism to be more viable, especially against habitat loss.  But you'll find that specialization increases efficiency.  The ocean vent dwelling extremophiles, for example, are anaerobic, meaning that they do not require O2 to keep their metabolisms going - in fact, I believe that O2 is toxic to them.  Most organism are aerobic, at least, they are after the Earth's atmosphere became 20% O2.  An organism that had one metabolic pathway that used oxygen and another that could function without oxygen would have an advantage in the greater range of habitats it could live it - but it takes more energy to keep two totally different metabolisms going.  So in oxygen, the aerobic organisms would have an advantage by not having to lug the dead wait of an entire energy system that is non-functional around O2, and anaerobic organisms for the same reason without oxygen.  Therefore, evolution favors speciation into two organisms, each to its own niche, as the best competitors.

Think of it this way: you're carrying around survival gear for every possible environment, while I am merely specialized for say, the desert we're in.  (I've reread Dune recently.)  We've both got moisture conserving tricks and ways to beat the heat in the day and the freezing temperatures at night.  You, however, are also lugging around a bulletproof vest, a spacesuit, a SCUBA mask, a snowsuit, and forest camo gear.  Guess who can get food while expending the least amount of energy?  Me, which means in the long run I'll have more energy to devote to my offspring.  Sure, you can handle outer space - but we're not in space.  So I win.

This. In fact, I might steal that last paragraph if I ever need to explain this to someone again. That is the perfect human example of generalization versus specialization, and why both exist. 

Now as for your idea about having a super-adaptable toolkit-like DNA, remember that mutations are random.  So if your organism could easily adapt by recovering its ancestral wings when those would be a net plus, it would be just as likely for it to recover its ancestral wings when they would do more harm than good.

Also remembering that we still aren't quite sure how much genetic drift, a completly random process, plays a role in all of this.

About organism becoming more complex over time... sorta.  Cells with mitochondria are more 'complicated' than cells without mitochondria, and they ded came later.  Multicellular organisms did come after single-celled organisms, and came before organisms with organs.  But then again viruses came after cellular life.

Do you know much about symbiogenesis theory for eukaryotic organism? Just interested, its been one of those things I've been excited about for years now.

ETA: Kai, I think it's pretty amazing that we have member dedicated to bringing us science news, identifying our insects, and explaining biology terminology.  Keep it up!

Thanks! I really love talking about it. Its one of the few things I'm good at.

[Elder Iptuous]

Very good.
I have realized in thinking about this short conversation that, although i have heard and, in fact, used many of these arguments against ID proponents (who, btw, i will never forgive you for lumping me in with,GA  ), that i have not really internalized the notion that it isn't progress due in no small part to the fact that i simply want it to be progress.  This is perhaps innevitable because of my engineering mindset that sees an iterative process that does not progress towards some ultimate goal (or, i guess, in the case of natural phenomena, along the direction of some motivating force) to be absurd, but that doesn't mean that it ain't so.....
I can perhaps assuage myself by focusing in on the definition that the goal of all life (as defined by myself) is "to live and reproduce as successfully as possible over an unbounded time frame and environment", on the key phrase "all life".  Would it be fair to say that life on this planet as a whole has been progressing (albeit with setbacks) towards this ultimate goal?

One last thread that i would like to snip is the genetic switch as mentioned.  In the analogy of the swiss army knife animal being more generally prepared for diverse environments, but not suited to outperform a specialist in a static environment, why would this apply to one whose genetic repetoire is not expressed in its form at any given time?  The only disadvantage that i can see to an animal having this hidden treasure box of features in waiting is that it would have more genetic material that something could go catastrophically wrong with, or that if it is a creature that does not breed/live in large numbers the possibility that features becoming expressed at innoportune times in a single individual would have a significant effect on the species as a population....  Perhaps you can think of another disadvantage that it would pose to justify it as not necessarily 'better prepared'. 
I guess the absurdly scifi 'ultimate creature' is imagining an organism with the features of a great deal of life as we know it in its genetics that are almost all not currently expressed.  It is currently of the form of a simple microorganism that is able to withstand the vacuum and radiative hazards of space, but upon landing upon a celestial body, a la panspermia thing, it would be able to develop the features that would allow it to thrive in whatever the habitat might be in relatively short time, without having to rely on random gene modification to reinvent the wheel.  sort of a genetically modular creature.....
Please do your best to cut that thread as it is unignorably tickling my brain...

[Kai]

Very good.
I have realized in thinking about this short conversation that, although i have heard and, in fact, used many of these arguments against ID proponents (who, btw, i will never forgive you for lumping me in with,GA  ), that i have not really internalized the notion that it isn't progress due in no small part to the fact that i simply want it to be progress.  This is perhaps innevitable because of my engineering mindset that sees an iterative process that does not progress towards some ultimate goal (or, i guess, in the case of natural phenomena, along the direction of some motivating force) to be absurd, but that doesn't mean that it ain't so.....
I can perhaps assuage myself by focusing in on the definition that the goal of all life (as defined by myself) is "to live and reproduce as successfully as possible over an unbounded time frame and environment", on the key phrase "all life".  Would it be fair to say that life on this planet as a whole has been progressing (albeit with setbacks) towards this ultimate goal?

One last thread that i would like to snip is the genetic switch as mentioned.  In the analogy of the swiss army knife animal being more generally prepared for diverse environments, but not suited to outperform a specialist in a static environment, why would this apply to one whose genetic repetoire is not expressed in its form at any given time?  The only disadvantage that i can see to an animal having this hidden treasure box of features in waiting is that it would have more genetic material that something could go catastrophically wrong with, or that if it is a creature that does not breed/live in large numbers the possibility that features becoming expressed at innoportune times in a single individual would have a significant effect on the species as a population....  Perhaps you can think of another disadvantage that it would pose to justify it as not necessarily 'better prepared'. 
I guess the absurdly scifi 'ultimate creature' is imagining an organism with the features of a great deal of life as we know it in its genetics that are almost all not currently expressed.  It is currently of the form of a simple microorganism that is able to withstand the vacuum and radiative hazards of space, but upon landing upon a celestial body, a la panspermia thing, it would be able to develop the features that would allow it to thrive in whatever the habitat might be in relatively short time, without having to rely on random gene modification to reinvent the wheel.  sort of a genetically modular creature.....
Please do your best to cut that thread as it is unignorably tickling my brain...

For that sort of thing to occur there would have to be some sort of environmental pressure for organisms to take that route. There is none. There likely will never be. Not only that, but it costs way too much energy to invest in such a thing compared to the abundant resources on this planet. An organism, more or less, IS a swiss army knife. Genetic variation with only isolated beneficial mutation is what leads to the majority of evolutionary modification on this planet. The creative possibilities of life are near endless within the structure of the original framework and given the time frame involved. Theres just no inertia, biological, behavioral or otherwise to set organisms out into space to seed other planets over time and space. Assuming microorganisms could get there, and there were ample resources, that is essentially all you would need to create the diversity of life on this planet over the same timescale. it would be wildly different, but it would happen, just not in the spectacular way you see it sci fi. I wouldn't hope. Rather, look to the amazing diversity on this planet. Here, Life is god, creation is occurring all around you.

Okay, so I get a bit spiritual about biology. Its part of who I am. A really interesting book I'm reading right now is Reinventing the Sacred by Stuart Kauffman. Its essential thesis is the movement towards creative nature = God, and uses arguments of biology being emergent and irreducible to physics, as systems that are doings rather than happenings, with individuals that posses teleos (will). It also contains lots of interesting science tidbits with philosophical leanings, and I haven't found anything thus far that would turn me off, no new agishness, no buzzwords.

Maybe thats right up your alley.

[Lupernikes_shadowbark]

but i'm not a biologist....i was being ironic only.....not seriously scientific

Its ooooooooooooooooooooooold.

And overdone. Please, I hear enough from creationists to make it so completely unfunny.

I also claim all right to abuse people for annoying me about this stuff, wallow in my mistakes and apologize for it later (if necessary).

fair enough, fair enough...I'm not a creationalist either just conscious, not of intelligent design (sneezes) but of perhaps some pattern to evolution, let's call it natural inclination to environment and stimuli or something along those lines.  We evolved but why only humans, why no other forms of life also?