Evolution Mechanics

Great Debates
1

First off, I would like to ask any foaming at the mouth Creationists to restrain themselves. Yes, I believe in God, but I’m hoping to keep this scientific and not have it devolve into a half-assed theological free-for-all.

The crux is this : My bachelors degree is in molecular biology but I have never bought the idea of random mutations and natural selection as the prime mechanism of evolution. That may work for bacterial populations, but seems far to random to produce wonders such as a bat’s ability to use echolocation. I believe there is another mechanism at work (some group of signal transduction pathways maybe?) that enables succesive generation to adapt to there environment. Call it “directed adaptation”. There is some support for this theory in the scientific community, but not a whole lot.

Ideas?
-Beeblebrox

“Pages one and two had been salvaged by a Damogran Frond Crested Eagle and had already become incorporated into an extraordinary new form of nest which the eagle had invented. It was constructed largely of papier mache and it was virtually impossible for a newly hatched baby eagle to break out of it. The Damogran Frond Crested Eagle had heard of the notion of survival of the species but wanted no truck with it.”

2

Well Beeblebrox, There is actually a signal transduction society, and a new wave of scientists and geneticists, putting a lot of stock in the new theories of signal transduction and directed adaptation. Ironically, last night there was a story on Discovery about the Neanderthals. And how Neanderthals didn’t actually become extinct because they were inferior to their superior African cousins, but infact they simply interbred and are part of our genepool today. They also spoke of the “Mitochondrial Eve” and how this species, our species actually came from a single species in our past. Not infact from different famuli but from the same group.

It is an interesting hypothesis, but it is still chaulk full of holes. I wonder if science will ever get to the point of knowing, what we want to know, in fact need to know…

3

I have no idea what you mean by “signal transduction mechanism”, but I’ll take a stab at your “crux”.

Darwin posited Natural Selection as the natural analog to human-directed “artificial selection” - the process of selecting desirable traits from a population, and breeding organisms with these traits in an effort to create something “new”. In nature, this “selection” is performed by, well, nature. Environmental influences, be they geographical, meteorological, ecological, or whatever, will dictate what traits will be passed on from generation to generation. Given enough time, this process, Darwin proposed, is what results in speciation (which is why he titled his book, “The Origin of Species”).

Beyond speciation, things get a little murkier. Strict Darwinists insist that Natural Selection will likewise result in differences between higher groupings (Genera, Families and Orders, for example, in the Linnaean hierarchy). Others believe that there is more at work then simply natural selection (the concept of “species selection” figures prominently here - the idea that there are factors which influence the differential survival of entire species, much like the way natural selection will influence the differential survival of individuals within a species).

One thing you need to understand, Beeblebrox, is the vast amounts of time involved. There’re a lot of intermediate forms between bacteria and bats. When you try to look at the starting point and the ending point, yes, it looks baffling. But, you have to take baby steps. Evolution, even if you take punctuated equilibrium into account, is a slow (by human standards), gradual process, and a million years is a very long time.

As for specifics, traits such as echolocation are not that difficult to understand, so long as you also understand the concept of “mosaic evolution” - the idea that not all traits will evolve at the same rate. Traits which we associate with bats did not necessarily evolve in tandem, with each subsequent generation gradually becoming more ‘bat-like’. Different parts evolved at different rates, and the sum of these parts results in what we know as a bat.

4

Darwin’s Finch wrote:
"Environmental influences, be they geographical, meteorological, ecological, or whatever, will dictate what traits will be passed on from generation to generation. "
Granted that’s true, but my question is how. We seem to looking at the same subject from two different perspectives (a very good thing when it comes to this type of discussion). You from the top down (speciation). Me from the bottom up (DNA and signal transduction).

Darwin didn’t even know what DNA was, so he never addressed the specific mechanics. The most common theory taught now is that random mutations (from uv light, carcinogens, viruses, basic cellular screw ups, whathaveyou) provide the genetic change that is the basis. From these shuffled cards, nature is dealt a hand and what works lives and what doesn’t dies. We know that the vast majority of random mutations don’t do squat. They either aren’t expressed or they end up expressing the same protein by a different codon. These won’t change even an amino acid.

Some, however, are expressed. Most of these do not change the protein’s function (it still ends up folding pretty much the same). The ones that do are frequently fatal. This seems like a lot of stillborne and aborted young to provide even the smallest change to have the remotest chance of providing a change to go through the natural selection filter. They make up for this by teaching that it takes place over millenia.

My problem is that there have been instances in the fossil record where there is an explosion of speciation in a relatively short time. So how about this: Maybe the DNA isn’t evolving like a drunken blind man trying to walk across a room full of furniture. Maybe information flow isn’t one way (DNA -> RNA -> Proteins). Maybe there is a mechanism to provide feedback. Maybe life on some level “knows” when its time and “decides” to start making changes. We are taught that there is no feedback besides natural selection on the organism (and up) scale. I think there is.

Maybe LeMark got it right for the wrong reasons.

Sidebar: How the @#$# does everybody gets the quotes to look like that. I know I’m new to these boards, but for the life of me I can’t figure it out.

5

One possible explanation for the “explosions” seen in the fossil record is that these occur during times of high environmental stress. During such times, there may be an increase over the background levels of genetic coding mutations, resulting in a larger pool for nature to select from (not meaning to anthropomorphize here; I just don’t know of any other concise way to state this). Another factor is what happens during development - it is well known that, genetic factors aside, stresses imposed during development can have a dramatic effect on the developing organism. Most often, these effects, like genetic mis-coding, are not advantageous. However, it is not inconceivable that some of these developmental changes are advantageous.

Another point to consider is that, even if you disregard the above, environmental effects act as filters for exsiting ‘background’ mutations. Suppose that a population will always produce a given set of mutations. The environmetal conditions present at the time will dictate which of these mutations are useful, which ones are neutral, and which ones are disadvantageous, thus, which ones are selected for. Even given the same pool of mutations, if the prevailing conditions were to change, the relative value of these mutations would then change as well, so natural selection would then act on a different set of these mutations.

Disclaimer: as you point out, we are looking at things from differing perspectives - my Bachelor’s degree is in Evolutionary Biology. As such, I have woefully limited knowledge of the intricacies of genetics; as such, any logical mistakes I make with regards to this topic are my own, not those of evolutionists in general.

As for the quoting aspect, you can click on the little “reply with quote” thingy under each post to see how to properly code quotes, bolding, italics, etc. You can also get a lot of help from the ‘About This Message Board’ forum.

6

Speaking strictly as a layman, since my degree is in chemical engineering, I view the “explosions” in the fossil record more as a function of competition. Most occur immediately after a mass extinction event, leaving plenty of room for new “experiments” by nature that normally would not have been able to compete with existing lifeforms. The Cambrian explosion was also distinguished by a lack of competition, since these were the first advanced multicellular lifeforms and they didn’t have to worry about existing competition.

7

(thanks for the tip on quotes, Finch)

I think we are in agreement to a degree. There should be an increase in coding mutations during times of stress.

Proteins relay “information” about the organism to the chromosomes regularly (this is signal transduction - A plant’s proteins might say something like “we need more chlorophyl!”) If there is a signal transduction pathway that activates a “dirty” replicating gene during times of stress (severe hunger, maybe?), that would account for the increased background mutations without violating the DNA -> RNA -> Protein model that is currently taught.

However, I still can’t let go of the idea that this is all that’s happening. It was less than 20 years ago that science had to revise the above and realize that sometimes information flows (RNA -> DNA). Retroviruses such as HIV prove this. Maybe info can flow: Proteins -> RNA -> DNA or even: Protein -> DNA. The proteins react with the environment and then relay to the DNA how and when to mutate. That’s the core of my idea.

O.K., but if these changes do not occur in the reproductive organs of the developing organism as well as the rest of it, then they wouldn’t be passed on to the generation that follows it.

No need to be so humble, Finch. I only have a Bachelors Degree in this stuff and am not currently working in the field. (There is only so many Equine paternity tests you can do before you think about a change in careers). Besides, my intelligence is probably more on par with the guy who invented the salad shooter than it is with Watson and Crick.

That could be true. To be honest, I don’t know enough about the fossil record. Some questions spring to mind though: What caused the mass extinctions? They weren’t ALL caused by impacts. Could accelerated adaptaion in a keystone species ripple outward? I’m thinking something like if a fungus evolves to be very good at killing bees. Bees die - plant species don’t get pollinated - plants die -herbivores that eat plants die… It would have to ripple out instead of going straight up the food chain, but you get the idea.

I think I will leave this for now. It is time to leave the office and go find a beer. If my next post sounds a bit squirelly headed, don’t worry, I’ll sober up in the morning.

-Beeblebrox

“Zaphod grinned two manic grins, sauntered over to the bar and bought most of it.”

8

Interesting question, may I throw something into the pot?

If you take two tobacco plants which require subtropical conditions, and move one of them to a temperate zone, it will just about survive, but it won’t thrive.

If it manages to flower and set seed, we might expect that, due to random mutations, some of the offspring may be better suited to slightly colder conditions, others would fail to grow; over many generations, we might expect that a cold-tolerant variety/species might emerge.

But what actually happens is (apparently) slightly different; if you collect the seed of the plant that was moved and grow them in the temperate zone, alongside the collected seed of the plant which we left where it belongs, nearly all of the seeds which were set in the temperate zone will produce plants better able to tolerate cold conditions than will the seeds collected from their native habitat.

After having said all that, I’m going to have to offer it as anecdotal; I can’t find the cite I was after, although I have read about this effect at least a couple of times in books about gardening history (not that this makes it true).

9

Beeblebrox wrote:

Mutations are random, sure, but natural selection? Natural selection is so not random it’ll make your head spin!

10

Jeez, of all the pedantic intelligent donkey things…

How about “natural selection and random mutations”?

There. Are you happy now? I hope so.

I think I read something along those lines, too. Hell, I think we studied it in Plant Physiology in college. Problem is I can’t remember much about it - but you might be on to something.

But maybe not. I seem to remember a “heat shock” gene grouping that allows seeds to do something similar. The thing is the seeds adapted, but their genetic code never changed. They were resistant all along, but the genes just weren’t expressed till they had to be, and the whole thing took time which is similar to your example. Memory is fuzzy though.

11

**

So far as I know, some species of bacteria are indeed known to increase their mutation rates under environmental stress. However, your suggestion above does nothing to explain the evolution of echolocation.

**

It’s a little unclear to me how such a system would work. You would need a way to do the following:

  1. Analyze the environmental stresses and formulate a creative solution. (Hmmm… not enough food? I know- echolocation!)

  2. Figure out what changes to the genetic program for development (at least in the case of metazoans) would be needed to produce that complex effect.

  3. Figure out which protein sequences would be needed to effect those changes. (At the very least, you would need a way of determining which amino acid changes would be required to change the binding specificity of developmental proteins like Hox or ftz. If the new proteins must serve radically different functions, the problem becomes much harder. If the proteins are to have new folds, rather than being simple modifications of existing proteins, then a single cell must have more computing power than a supercomputer in order to pull it off.)

  4. Back-translate the protein sequence into a DNA sequence.

  5. Hope the whole complex mess works in one try, since- unlike in natural selection- near misses get you nowhere.

I’m unfamiliar with the “signal pathways” which are suggested to cause directed evolution. Could you go into more detail?
If I might make a few more points:

  1. Many of the proteins involved in embryogenesis and cell-cell communication (which are necessary for the existence of multicellular organisms) are the products of exon shuffling, which pieces together functional units of old proteins in order to make new ones. Exon shuffling originated around the time of the Cambrian explosion, so there’s no need to invoke “directed evolution” to explain it. The enormous advantage produced by exon shuffling is presumably what caused metazoan evolution to take place so quickly.

  2. Have you read Wonderful Life? It has a number of things to say about mass extinction and the Cambrian explosion, none of which involves directed evolution.

  3. Acquired characteristics (such as the tobacco plant example) can be inherited in special circumstances. For example, there’s the URA3 and PSI+ traits in yeast, which are passed on to offspring through prions rather than through DNA. However, these changes are simple on-off switches, which can’t lead to full evolution.

  4. Have you read Cells, Embryos, and Evolution? I’m a quarter of the way through it now, and I think it would be right up your alley. It explains a great deal of molecular biology in terms of evolution, and apparently later chapters deal with metazoan evolution.

-Ben

12

Much of this thread is based on the otherwise astute Beeblebrox’s unjustified assumption that there ever was any such thing as a speciation “explosion”! There is very little evidence of such an event.

Yes, I know: you’re probably all thinking about the so-called “Cambrian explosion”. As popularly understood, this is quite a misnomer, spread through the public perception primarily by the doubtable (not redoubtable) Stephen Jay Gould and bad pop-science books and TV shows. It is true that there was an apparently “sudden” (if you consider something occurring over a period of 10 million years “sudden”) and dramatic increase in the number of fossils dating from that period, but this certainly does not mean that there was a corresponding “explosion” in species! That may sound reasonable at first glance, but it is fundamentally flawed.

All that has been scientifically established, to tbe best of my layman’s knowledge, is that a forerunner phylum that could finally leave fossils began to appear at that time. Prior to that time, very few species left any physical record. For all we know, the Cambrian may well have been a period of unprecedented extinctions of non-fossilizable species, leaving only a few paltry survivors that were eventually to give rise to the new phyla we see in the fossil record.

Furthermore, our friend Beeblebrox seems to invert the “tree” of evolution. It must always be viewed upside down, with the trunk at the historical “top”, branching out down below as time progresses. Gould and others occasionally seem to lose sight of this, and sometimes seem to postulate an “explosion” of phyla starting off out of the blue as if from nothing!

There is nothing at all to suggest that standard neo-Darwinism cannot account for everything we see using slow, gradual processes.

13

As I alluded to above, Stephen Jay Gould simply cannot be considered a reliable source of knowledge on the Cambrian “explosion” (not to mention other topics). Wonderful Life is beautifully crafted misinformation. Don’t trust it.

For discussion of this and other questions surrounding Gould’s opinions, see Richard Dawkins’ Unweaving the Rainbow, particularly the chapter “Huge Cloudy Symbols of a High Romance”, and also the new edition of Dawkin’s The Selfish Gene.

14

Merely an example of the complicated systems involved.

Obviously

Hah!

And the Nobel Prize goes to…

Got news for you, it does.

But which sequence? Do you even know what a codon is?

Look up “signal transduction”. If you research it you will soon realize that it is most likely going to to take chaos theory to figure it out. We only know a few of the chemical pathways (these are chemical reaction “chains”). In signal transduction you are going to see a whole bunch of kinases. That means enzymes that transfer potasium. This is the most common signal among proteins within a cell. There are millions of different enzymes within one cell. At the moment, science can only play “follow the potasium” to figure it out. With millions of different paths, a particular Potasium can travel in incalculable ways. This is obviously a net with info flying every which way.

Word of advice: If you are going to post something with such a condescending tone…

you should at least know what the Hell you are talking about.
Now that you have been good and flamed, there is one thing in your post that is relevant. “Exon Shuffling” By this I assume… (wait, what the hell? I’m not sure you know what that is either.) I will discuss it anyway.

Ben, an exon is the piece of a gene that is expressed.

For the sake of the laymen I WOULD like in this discussion (Darwin’s Finch, hardcore, Magnetout, and anyone else on the boards who isn’t a pompous ass) I will not go into the esoterics of promoters and operons. (Finch, if you are reading this, know that I want your opinion. I am a molecular biologist looking at the mechanics of evolution. The opinion of an evolutionary biologist is invaluable. We don’t speak quite the same language, but we may both learn alot.)

There are two things besides random mutations that cause genetic change and are not part of my admitedly speculative hypothesis. The first is transposons. These are gene sequences that disassociate from the chromosome and then reattach in a different location. Nobody knows why this happens. BUT THAT IS PART OF MY POINT.

The second is called “crossing over” and happens during meiosis. This is sex. “Higher” animals are diploid (that means that they have two sets of chromosomes, Ben) and their gametes (sperm and eggs) are haploid and have one set. The haploid cells must come from diploid cells. The two chromosomes of the haploid cell come together, trade pieces, and it divides leaving the gamete and a “daughter” cell which is destined to die.
-Beeblebrorox

“I’m a pretty dangerous dude when I’m cornered.”
“Yeah, you go to pieces so fast people get hit by the shrapnel.”

15

Now you, Ambushed, are somebody I can disagree with and still respect.

I think you might have missed where I am coming from, though. This thread is not actually based on any speciation explosion. It is based on the mechanics of the cell itself. I am trying to work from the bottom up. Trying to get “under the hood” of evolution. I am hoping I can get help from the top, bottom, side, whatever.

I have always hated the “tree” analagy. The ecology of any given time is interconected and not much different from the one that follows it…

There have been explosions, though. I am not a student of the fossil record but I know it has happened. “Sudden” changes can happen. Flowering plants took over the Earth very, very quickly. Or so I seem to remember.

16

Yeah, so next time somebody gives me shit about smoking and cancer I’ll just say, “Look babe, I’m not killing myself, I’m evolving.”

17

Beeblebrox: First of all I had to check your username three times, in order to spell it right :smiley: . 'course maybe that just speaks to how sharp I am this morning :wink: .

This, to the best of my meager knowledge, is the source of the bulk of genetic diversity in sexual organisms. NOT random mutations, which are not terribly common in “higher animals”, with useful mutations being particularly rare. Not saying that mutations are not sources of genetic diversity and material adaptation, just that they are much less significant for sexual beings. The reason we see the impact of mutation so readily in bacteria and the like is because of the incredible proliferation in numbers and the rapid generational turnover.

By contrast parthenogenetic species of animals, because of their slow reproductive rates ( relative to bateria and whatnot ) are generally considered to be likely evolutionary “dead-ends”. Or at least in a sort of “evolutionary stasis”. Of course many organisms are facultatively parthenogenetic ( and I probably don’t need to point out that sex is not exclusive to “higher animals” :wink: ), which gives the flexibility to explore the advantages of both ends of the spectra. In non-arthropod animals this is generally not the case, however. Rather in herps and fish, parthenogens tend to result from hybridization events ( sympatric speciation ) and are fixed parthengens or gynogens, often with variable ploidy counts ( often triploid, a nitpicky and not particularly relevant exception to your assertion above :slight_smile: ). Which begs the question of whether backcrossing parthenogens with parental species can create novel non-parthenogentic species ( tetraploid perhaps ). There is some suggestion that at least individuals such as that exist.

All of which is crawling farther and farther afield from my point and Darwin’s Finch has already seen me regurgitate this stuff before, anyway :stuck_out_tongue: .

At any rate, my point is just that you cannot just look to mutations under stress as the predominate source of genetic diversity in most higher organisms - the generations turn over too slowly and mutations are too infrequent to provide much purchase for Natural Selection.

As another not particularly relevant aside, I agree with ambushed that Wonderful Life is badly flawed, though well-written. For one reason he attaches entirely too much significance to the word “Phylum”, forgetting that it is merely a made-up hiearchical placeholder that is not comparable in significance across groups.

  • Tamerlane
18

Zaphod, it’s rarely profitable to respond to perceived insult with additional insult. And this forum is not the place for flames.

19

A small correction to my earlier post. Mutations may be common, but it is significant mutations that are not. Most mutations don’t do diddly and are not expressed in phenotype in any respect. Just to clarify :slight_smile: .

  • Tamerlane
20

Beeblebrox said:

One problem with this hypothesis in higher animals is that in order for this to work, the gametes (which don’t normally participate in the organisms own survival) would also have to be affected, as you pointed out earlier to Darwin’s Finch. Could you clarify how this might occur and for what reasons (i.e. why would such a message be directed to the gametes, where they can not help the organism sending the signal)?

Beeblebrox also stated:

Did you mean to say phosphates? While kinases certainly may act upon potassium (K) channels, among other targets, they transfer phosphates, not potassium.

Ben, did you mean proteins? I thought prions were misfolded proteins that cause plaques and holes to form in the brain, like new variant Creutzfeld-Jakob disease, mad-cow, kuru, and scrapie.