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Author Topic:   Question on how Evolution works to produce new characteristics
Dr Jack
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Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
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Message 6 of 104 (563609)
06-06-2010 5:12 AM
Reply to: Message 5 by Europa
06-06-2010 4:38 AM


My question is, if the frogs with the hint of an orange speckling survive more and make this the dominant trait of the population, will it not be a response to a 'felt need'? (Lmarkism?)
If the froggies on the other hand go extinct, will it not be because they could not respond to the 'felt need'? The 'felt need' being getting themselves orange speckled.
No. There's not 'felt need' effect going on.
Suppose there's your all-green frog population. This is because all of the various genes involved work together to produce green. If they are to get orange speckles they require a gene to emerge that produces the right pigment, or a change in the distribution of the green pigments that produces an orangey result.
This will happen (or not happen) because, just by chance, there is a mutation in the genome of a particular frog. This is no more likely to happen when the mutation is "needed" than when it is not needed.
In the new environment the speckled frog, and all of its offspring that carry the gene, will have a selective advantage over the green frogs so slightly more of them will survive to the next generation. Had it happened in the all-green environment then the new mutation would be selected against, and tend to die out.

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Dr Jack
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Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 10 of 104 (563613)
06-06-2010 5:39 AM
Reply to: Message 8 by Europa
06-06-2010 5:31 AM


1. Why do you say this -- orange speckling -- isn't Lamarkism?
Lamarkism is the inheritance of derived traits. It would be a frog somehow "learning" how to have orange speckles during its lifetime and then passing that trait onto its offspring
2. If orange speckling, by chance, occurs due to a single mutation on a single frog, will it be capable of making this the dominant trait of the colony over time? Is this how evolution works? I mean by the chance mutation of a favourable trait on a single organism?
Yes - mathematical modelling shows that a dominant trait that emerges in a single organism can reach fixation even if it only provides a slight fitness advantage - and yes and yes; but it's a bit more complicated than that.

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 Message 8 by Europa, posted 06-06-2010 5:31 AM Europa has replied

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


(1)
Message 12 of 104 (563616)
06-06-2010 6:22 AM
Reply to: Message 11 by Europa
06-06-2010 5:49 AM


The often quoted example of Lamarkism is the elongation of a giraffe's neck. Now, the giraffe did not 'learn' how to have a long
neck. But this is Lamarkism.
The Lamarkian notion was that the giraffe got a longer neck because during the lifetime of a giraffe they would strain to reach higher leaves, and in doing so slightly lengthen the neck, and then pass this slightly lengthened neck on to their offspring. You'll note that a) animals necks don't actually get longer by straining to reach things and b) even where traits can be environmentally acquired they are not passed on to the offspring*.
How is the orange speckling of the froggies any different?
If the frogs could acquire their orange speckles from the environment, and then pass this acquired characteristic on it then it would be Lamarkian. If they are born with orange speckles because of a mutation, and then pass that mutation on to their offpsring, it is Darwinian.
* - epigenetics aside. But that's a very limited case with preset limits.

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Dr Jack
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Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 28 of 104 (563862)
06-07-2010 5:13 AM
Reply to: Message 21 by Europa
06-06-2010 11:19 PM


Re: Drift And Selection
If this is so, how do you explain living fossils?
Do they not mutate?
Firstly, recognise that living fossils are the exception, not the rule. Secondly, note that living fossils are not identical to their fossil relatives, merely similar and, finally, recognise that the evidence suggests that living fossils are genetically quite different from their ancestors suggesting that they have mutated but stablising selection has kept their phenotypes consistent.
It cannot be that their environment did not change. So, if they mutate and if their environment changes, why are they the same?
Why can't their environment have been unchanging? Or, more saliently, why can't the aspects of it relevant it their survival have been unchanging? Remember, as well, that environments are not spatially unvarying, species can move to areas that continue to match the environment they are fit for as well as adapting to their current environment.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 54 of 104 (564229)
06-09-2010 5:22 AM
Reply to: Message 52 by RAZD
06-08-2010 9:37 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
Now here we have a bit of a conundrum: we have a fossil organism\species\type that has apparently evolved tremendously - they have apparently evolved into all other forms of life (or certainly a large number of them)
I'm pretty sure this is incorrect. If you look at phylogenies of life, the cyanobacteria group with other cyanobacteria, they're not intermixed with other bacterial groups, and bacteria are quite distinct from archaea and eukarya. So it's generally believed that the Archaea/Bacteria split predates the separation of cyanobacteria from other bacteria.
(If you look at the tree here, all the cyanobacteria are grouped between 4 and 5 O'Clock from Gloebacter and Synechococcus. Note how the root for this group nests with others.)
Edited by Mr Jack, : Added tree of life

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 56 of 104 (564383)
06-10-2010 7:52 AM
Reply to: Message 55 by RAZD
06-10-2010 7:39 AM


Re: Cyanobacteria -- the ultimate "living fossil"?
Perhaps. Or perhaps you are confusing the status of modern cyanobacteria with what the status of ancient cyanobacteria would be.
No, I'm not.
Curiously, you can also make a straight line from original hypothetical ancestor population (at the center) to these modern cyanobacteria, with all else branching off that line.
Er, no. If cyanobacteria were the stem group for all the rest you'd expect other groups to group within, with some cyanobacteria more closely related to other groups than they are to other cyanobacteria. Consider the reptiles for an example of how this works.
Also the root is not arbitrary. You can't just root a phylogeny anywhere you like.
Which would then need to be before 3.5 billion years ago, yet the only evidence is that cyanobacteria existed at that time ... or that the bacteria lineage split off from the cyanobacteria lineage later ...
Actually there is chemical evidence for Archaea back to 3.8 billion years ago. The evidence for cyanobacteria is more solid because they are involved in stromatolite formation making the preservation of fossils indicating their morphology more likely.
Edited by Mr Jack, : No reason given.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 91 of 104 (564600)
06-11-2010 5:21 AM
Reply to: Message 81 by RAZD
06-10-2010 7:54 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
So logically you start with the oldest known life form. Cyanobacteria.
No, you apply cladistic principles to produce the most parsimonious tree. Using incredibly scant fossil evidence to imply positioning is unwise.
Logically this means (many) other forms of life have branched off from this lineage rather than the other way around.
No, it doesn't. And the genetic evidence counters your position. If cyanobacteria were the root, we'd expect to see cyanobacteria interspersed with the other groups. We don't. We see them all group together.
Do you have any supporting evidence other than some of the earliest fossils being cyanobacteria? Is this an idea you've picked up from anywhere in the scientific literature or is it one of your own?
There is possible evidence of some kind of life, yes. IIRC you objected to use of this evidence for life on another thread ...
There's specifically evidence of Archaea. Their different membrane lipids leave different traces in the record. And I believe you recall incorrectly.
And amusingly, none of your issues affect the argument that cyanobacteria is the oldest living fossil.
Yes, it is. I never said it wasn't. I objected merely to your completely unsupported assertion that large portions of modern life evolved from cyanobacteria, which is untrue. Unless you want to consider the endosymbiosis of cyanobacteria in the Eukaryotic photosynthesizers as such.

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 Message 92 by RAZD, posted 06-13-2010 2:01 PM Dr Jack has replied

  
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 93 of 104 (564887)
06-13-2010 3:39 PM
Reply to: Message 92 by RAZD
06-13-2010 2:01 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
Can you show that it is absolutely impossible for all life to have evolved from cyanobacteria? If you cannot falsify the possibility, then it exists.
It is possible that all life evolved from cyanobacteria, it's just not a position that is supported by the evidence. And, despite your frothing, you're the one making a positive assertion that everything evolved from cyanobacteria.
Curiously, genetic evidence cannot tell you when species diverged nor what the actual species they diverged from was, only that it was a shared common ancestor at some point in the past.
Except that's not true. There's these things called molecular clocks. Not that that's particularly relevant, since what we're talking it is the order of branching, and the status of various clades.
The genetic results are the same, based on the information available ... from living species.
Yeah, your simple branching pictures are cute but have bugger all to do with we're talking about. Consider instead of species B as your starting point, species B and it's sister species C, both in this case cyanobacteria, if all life had evolved from cyanobacteria we'd expect to see cyanobacteria more closely related to other life than they are to other cyanobacteria. If A' and B' evolved from B, and C' evolved from C, A' (not cyanobacteria) should be closer to B' (cyanobacteria) than B' is to C' (cyanobacteria). This isn't the case! All cyanobacteria group together, no cyanobacteria group with other organisms, this suggests that cyanobacteria are monophyletic and branched from the rest of life as a group.
You see the remaining traits of modern cyanobacteria all grouped together. We classify these traits as being ones belonging to cyanobacteria because they the traits that are common to the modern species of cyanobacteria and not to other life forms.
The tree I showed you is based on ribosomal DNA, it is not based on morphological traits.
Thus the common ancestor could be a cyanobacteria ... unless you can show some reason why not.
It could be. Apart from the complete lack of support for your assertion, and the fact that it is more parsimonious with the known evidence to think that the divergence of Archaea and Bacteria predates the emergence of cyanobacteria and, indeed, that the major Bacterial lineages diverged before cyanobacteria emerged.
Which brings us to this:
Curiously, I find that genetic assumptions on when certain divergences occurred are no good if they do not correlate with fossil evidence. In other words, if the divergence occurred after 3.5 billion years ago, then cyanobacteria are the most parsimonious ancestors.
1. Cyanobacteria are not certain to have lived at 3.5 billion years ago, we think they do, because we've found stromatolites and stromatolites are thought to be formed by cyanobacteria but there are no direct trace fossils of cyanobacteria from this time. The earliest definite traces of cyanobacteria are later.
2. The only reason we know cyanobacteria existed at this time is that they leave stromatolites which are macro-scale structures we are able to identify at this period; picking on something which is extremely likely to be a preservation artefact and basing a theory on it is silly.
3. The earliest traces of life we have aren't cyanobacteria, they're Archaea. Now, these aren't solid enough to say for certain that Archaea predate other life, but at least this - unlike your assertion about cyanobacteria - is consistent with information from other sources.
At the very least you have to concede that your notion is your own speculation whilst the consensus view is very much not in agreement with you.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 96 of 104 (565163)
06-15-2010 6:56 AM
Reply to: Message 94 by RAZD
06-13-2010 6:02 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
Hi RAZD
... OR that the evolution cyanobacteria has resulted in a large part of life as we know it.
Again, it's possible but it's unlikely and unsupported by the available evidence.
Curiously, I did not say morphological. It seems you have made another mistake in reading. Nor does this (corrected) statement contradict what I said, quoted again above.
Unless A'' etc. descendants diverged more from the ancestral population than the B'' and C'' descendants -- losing cyanobacterial classing traits in the process -- in order to take advantage of a different ecological opportunity.
My apologies, you did not say morphological. However, the essential point remains; the tree is based on ribosomal data none of the traits used to identify cyanobacteria are used to make the tree.
This means that there is likely NOT a strict lineal line of descent from early organisms to the life we see today, but rather that the lineages likely crossed and crossed again, sharing traits before settling down.
Yes, this is true and it continues today. And if all you're suggesting is that some genetic material has transfered from cyanobacteria to many other forms of life alive today then, yeah, you'd probably be correct - but no more correct than if you pick any other kind of life. If you want to assert that that most life traces its ancestry in a more substantial way to cyanobacteria then you are probably wrong.
That's pretty strong evidence that the first known life were responsible for the formation of stromatolites.
1. It's evidence that stromatolites were made by life, something I've never disputed. It does not negate the various evidences of life that predate the stromatolites.
2. Even ignoring 1, there is zero evidence that stramatolites were actually formed by the first life, as opposed to the first known life. Stromatolites have been found because they are macrostructures resistant to destruction by geological processes. Rocks that old are rare, rocks that old that would preserve solid evidence of life that isn't forming stromatolites have not yet been found.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 97 of 104 (565165)
06-15-2010 8:24 AM
Reply to: Message 95 by xongsmith
06-14-2010 6:09 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
I think we have to consider probability theory and things like Maximum Likelyhood...and I think Mr. Jack was arguing that this evidence of stromatolites - while supporting the notion of cyanobacteria being the earliest known life forms - was not necessarily evidence that it was the oldest life form.
Indeed.
The question might be: where does C attach to the tree? There are 2 little possible marks shown here. C attaching to the A leg is not diagrammed out for clarity. We do know that C does attach somewhere. Above or below the branch. Correct me if I'm wrong, but I think Mr. Jack is only arguing that, on a molecular basis, it looks like "below" is more probable?
Not quite and we need some more branches to illustrate:
+----A
               |
          +----|
          |    |
          |    +----C1
          |
o----c----|
          |
          |
          |    +----C2
          |    |
          +----|
               |
               +----C3
Here, o is the original life, c is the ancient cyanobacteria. C1-3 are living cyanobacteria and A is another kind of life. This represents either of RAZD's suggestions. What you'll note is that A is more closely related to C1 than C1 is to either C2 or C3 (i.e. cyanobacteria are non-monophyletic). Now, obviously, we don't have the actual tree to look at, we can only reconstruct it from the data we have. One of the best ways to do this when we're looking at things on this kind of timescale is ribosomal DNA because ribosomes have a very low mutation rate, and - as far as we can determine - the changes are primarily non-selective, certainly when looking at groups within, say, the bacteria.
This data, should, if the tree above is what's happened find that some cyanobacteria living today are more closely to related to some non-cyanobacteria living today than they are to other cyanobacteria. Which is the primary way of identifying non-monophyletic clades. That isn't what we find: all cyanobacteria group together, suggesting that they are monophyletic.
Now, it's possible that this data is misleading. It could be for a number of reasons: this is based on statistical chance and it could have just so happened that cyanobacteria happened to have had mutations that hide the real facts but that's unlikely or it could be that the entire branch of cyanobacteria that diverged into other life completely died out, leaving a monophyletic branch to remain. These things are possible, but they're not the most parsimonious interpretation of the data available to us - which is that cyanobacteria are monophyletic and thus that cyanobacteria have no non-cyanobacterial descendants alive today.
Pictorially:
+--C1
           |
   +--c----|
   |       |
   |       +--C2
o--|
   |       +--A1
   |       |
   +-------+
           |
           +--A2
Where C1 & C2 are living cyanobacteria and A1 & A2 are other forms of life. Note the division between these lifeforms and C1 & C2 comes before c - the fossil cyanobacteria.
Note also that this is based on the interpretation of differences not on any rate based changes, relative or otherwise.

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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 99 of 104 (565328)
06-16-2010 4:39 AM
Reply to: Message 98 by RAZD
06-15-2010 11:39 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
Yes, that's the "or it could be that the entire branch of cyanobacteria that diverged into other life completely died out, leaving a monophyletic branch to remain" possibility. It's not as parsimonious an interpretation of the data.
The most parsimonious explanation is that the tree constructed from the genetic data is the actual evolutionary tree, that being how the tree is constructed and all*. To sensibly reject that interpretation you'd need strong evidence, which you don't have.
* - Within certain limits, that aren't relevant to the case at hand.

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 Message 101 by RAZD, posted 06-16-2010 7:13 PM Dr Jack has replied

  
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 102 of 104 (565476)
06-17-2010 4:33 AM
Reply to: Message 101 by RAZD
06-16-2010 7:13 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
Or it simple became the branch of life that we define as non-cyanobacteria, based on the differences in traits from the branch that we define as cyanobacteria.
No. Because you're talking about populations here, not individuals. The pictures we're drawing are vastly simplified pictures, the real picture involves vast bushy trees of many, many individuals. To produce the picture that we observe from the possibility you suggest involves the extinction of many, many intervening lines. That's much less likely than the possibility that what we observe is correct.
When you do your "most parsimonious" tree constructed from the genetic data you will end up with (surprise) the very same results you keep nattering on about, because what is used to differentiate between the A lineage and the C lineage are the traits that they do not have in common.
Once again. This is not so. None of the genetic traits used to construct the tree are used to distinguish cyanobacteria from non-cyanobacteria. That's why ribosomal DNA is used.
Or just realize that genetic analysis does not make a complete picture, especially at this 3.5 billion year remove from early life ... life for which we have absolutely no genetic data ... and as a result it is incapable of saying whether the divergence into A and C happened before or after the date of the fossil evidence we have for B.
Genetic analysis is imperfect but it is by far the best technique for dealing with situations such as these.
As opposed to no existing evidence for some made up ancestor, and ignoring evidence that B lived 3.5 billion years ago?
The evidence is twofold: first, the evidence of Archaea predating the stromatolites by 300 million years and, second, the evidence that the lower branches of the tree predate the split to the cyanobacteria. The cyanobacteria, according to the best evidence we have, are monophyletic. That means that the rest of life did not spring forth from them.
The issue is whether this occurred before or after B, and all I'm saying is that we don't know. Genetic information doesn't tell you dates, so it cannot produce the answer, the answer will come from fossil evidence, if evidence becomes available at all.
Again, genetic evidence does not need to give dates to determine the order of splits.

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