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Author Topic:   Question on how Evolution works to produce new characteristics
Mr Jack
Member (Idle past 327 days)
Posts: 3475
From: Leicester, England
Joined: 07-14-2003


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.


This message is a reply to:
 Message 81 by RAZD, posted 06-10-2010 7:54 PM RAZD has responded

Replies to this message:
 Message 92 by RAZD, posted 06-13-2010 2:01 PM Mr Jack has responded

  
RAZD
Member
Posts: 15818
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 1.8


Message 92 of 104 (564883)
06-13-2010 2:01 PM
Reply to: Message 91 by Mr Jack
06-11-2010 5:21 AM


Re: Cyanobacteria -- the ultimate "living fossil"?
Hi Mr. Jack,

Amusing. I notice that you did not provide an answer to this simple request:

quote:
If you can point to a node as say that THIS divergence occurred at ____ billion years ago, and before that there were no cyanobacteria, then please do so.

Do you have any supporting evidence other than some of the earliest fossils being cyanobacteria?

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.

No, you apply cladistic principles to produce the most parsimonious tree. Using incredibly scant fossil evidence to imply positioning is unwise.

So you discard the evidence and replace it with hypothetical inventions? Fascinating approach to science.

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.

Until you have fossil evidence of other life forms, and can date when they first lived, then you have no means to gauge which came first. It could be A, it could be B ... (or it could be a group of different species), at this point we don't know.

... And the genetic evidence counters your position. ...

Ah yes, the gods of genetic evidence cannot be disobeyed.

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.

   \A
\
/\
B'/ \A'

Species A evolved into Species A' and Species B'

     B/
/
/\
B'/ \A'

Or Species B evolved into Species A' and Species B'

The genetic results are the same, based on the information available ... from living species. In neither case can you tell what the common ancestor was (or was not), only that it was a common ancestor and had traits, some of which are common to both daughter populations and some of which are only common with one or the other. The descendants of the daughter populations will also add new traits that are not common with the other daughter population (unless horizontal gene transfer is involved).

(Plus, as noted, we have the problems of the entertwined roots of life: mitochondria and chloroplasts are distinctive elements to most multicellular eukaryotic life, and the genetic evidence is that cyanobacteria contributed to these lineages as well.)

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.

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.

You also see cyanobacteria grouped with other bacteria (etc) based on their shared genes, which come from the common ancestor. How do you know that those traits are not also ancient cyanobacteria traits?

Thus the common ancestor could be a cyanobacteria ... unless you can show some reason why not.

If you can point to a node as say that THIS divergence occurred at ____ billion years ago, and before that there were no cyanobacteria, then please do so.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 91 by Mr Jack, posted 06-11-2010 5:21 AM Mr Jack has responded

Replies to this message:
 Message 93 by Mr Jack, posted 06-13-2010 3:39 PM RAZD has responded

  
Mr Jack
Member (Idle past 327 days)
Posts: 3475
From: Leicester, England
Joined: 07-14-2003


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.


This message is a reply to:
 Message 92 by RAZD, posted 06-13-2010 2:01 PM RAZD has responded

Replies to this message:
 Message 94 by RAZD, posted 06-13-2010 6:02 PM Mr Jack has responded

  
RAZD
Member
Posts: 15818
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 1.8


Message 94 of 104 (564927)
06-13-2010 6:02 PM
Reply to: Message 93 by Mr Jack
06-13-2010 3:39 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
Hi Mr. Jack,

... And, despite your frothing, ...

ooo ad hominems now?

... you're the one making a positive assertion that everything evolved from cyanobacteria.

Curiously, you are missing something. Fascinatingly I've repeated it to see if you would see it the second time.

quote:
Message 52: 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 wonder how much you enjoy making mountains out of molehills.

... you're the one making a positive assertion that everything evolved from cyanobacteria.

Actually you have agreed with what I said:

It is possible that all life evolved from cyanobacteria, ...

... OR that the evolution cyanobacteria has resulted in a large part of life as we know it.

There's these things called molecular clocks.

That are absolutely useless in determining dates for when things occurred. The molecular "clocks" are only as good as their calibration to dates provided by fossil evidence.

Not that that's particularly relevant, since what we're talking it is the order of branching, and the status of various clades.

Oh, but it is very relevant to your claim of having genetic evidence that contradicts the possibility of cyanobacteria being a common ancestor.

Genetic "clocks" are relative dating mechanisms that can tell you that A happened before B which happened before C, but not when they actually happened. No better than geological formations can give you relative dates for fossils in different strata.

We also know that the rates of evolution change in different circumstances, and thus we know that any assumption of a steady rate of change is false. All one needs do is compare the different "clocks" in different species to see that they do not produce - cannot produce - a uniform rate of change.

Yeah, your simple branching pictures are cute but have bugger all to do with we're talking about.

Which shows that you missed the point.

quote:
The genetic results are the same, based on the information available ... from living species. In neither case can you tell what the common ancestor was (or was not), only that it was a common ancestor and had traits, some of which are common to both daughter populations and some of which are only common with one or the other. The descendants of the daughter populations will also add new traits that are not common with the other daughter population (unless horizontal gene transfer is involved).

The tree I showed you is based on ribosomal DNA, it is not based on morphological traits.

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.

... 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.

And you still have not pointed out evidence that shows when this occurred, rather it is all conjectural and hypothetical.

It is also generally considered that there was considerable mixing going on in early unicellular life, with lots of traits being traded back and forth, and there is some disagreement whether archaea are a separate clade (see below).

And this still does not mean that cyanobacteria are not responsible for major portions of life as we know it.

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.

Okaay, then lets say we are talking about "stromatolitia" - ancient organisms that created the stromatolites (mats of organisms periodically buried by sediment, building up layers that fossilized) 3.5 billion years ago - and that we have descendants today that still produce stromatolites in much the same way that these 3.5 billion year old ancestors did.

These modern descendants happen now to be classified as cyanobacteria, because they happen to be ONE descendant branch from the early "stromatolitia" ... but they are still "stromatolitia" (because dogs are still dogs eh?).

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), AND

we have a fossil organism\species\type that has apparently barely evolved any changes at all from the original ancestral population, AND

they evolved from the same population of organisms.

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.

Is it? Or are there some questions involved

quote:
Message 81: ps - another good source on the tree of life is

http://www.tolweb.org/tree/
http://www.tolweb.org/Life_on_Earth/1

quote:
The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life. We hope to provide a comprehensive discussion of these issues on this page soon. For the time being, please refer to the papers listed in the References section.

And there is also the issue of horizontal gene transfer mucking up the roots ...


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.

The evidence is that this was going on after 3.5 billion years ago. This also means that any type of organism from that period could be a "father" (donor of genetic material) rather than a "mother" (provides the cellular structure for the offspring of the combined genetic material).

Certainly we do not classify all the plants with chloroplasts as cyanobacteria, even though genetically they nest together.

The question is whether there are other traits that come from cyanobacteria that are not classified as cyanobacterial traits even though the "stromatolitia" may well be the original source.

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!

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.

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.

And you call my position speculative.

What you have are chemicals that may (or may not) be from early life forms. It could be evidence of evolving life, agreed, however to classify it as belonging to one form of life over any other, with nothing else to go on than hypothetical constructions, is pure speculation.

http://www.astrobio.net/.../evidence-of-earths-earliest-life

quote:
"We already knew from our earlier work that we had an assemblage of stromatolites that was most plausibly interpreted as a microbial reef built by Early Archean microorganisms," adds Allwood, "but direct evidence of actual microorganisms was lacking in these ancient, altered rocks. There were no microfossils, no organic material, not even any of the microtextural hallmarks typically associated with microbially mediated sedimentary rocks."

So Allwood set about trying to find other types of evidence to test the biological hypothesis. ...

What she saw were "discrete, matlike layers of organic material that contoured the stromatolites from edge to edge, ...

Allwood says she, Grotzinger, and their team have collected enough evidence that it's no longer any "great leap" to accept these stromatolites as biological in origin. "I think the more we dig at these stromatolites, the more evidence we'll find of Early Archean life and the nature of Earth's early ecosystems," she says.


That's pretty strong evidence that the first known life were responsible for the formation of stromatolites.

Enjoy.

Edited by RAZD, : clrty, end added


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 93 by Mr Jack, posted 06-13-2010 3:39 PM Mr Jack has responded

Replies to this message:
 Message 95 by xongsmith, posted 06-14-2010 6:09 PM RAZD has acknowledged this reply
 Message 96 by Mr Jack, posted 06-15-2010 6:56 AM RAZD has acknowledged this reply

  
xongsmith
Member
Posts: 1372
From: massachusetts US
Joined: 01-01-2009
Member Rating: 1.4


Message 95 of 104 (565092)
06-14-2010 6:09 PM
Reply to: Message 94 by RAZD
06-13-2010 6:02 PM


Re: Cyanobacteria -- the ultimate "living fossil"?
That's pretty strong evidence that the first known life were responsible for the formation of stromatolites.

...so far.

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. He says:

... 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.

Now when he's saying "more parsimonious", I take it to mean "more likely". His evidence is at the molecular level, where I have no expertise. Are we talking 12% versus 11%? 52% versus 31%?
x% versus y% where all we may suspect so far is that x is greater than y, because it's more likely?

let's look at this:


O
\
\'
\
/\ ?
/ \' \
/ \ \
A B C

O = common ancestor
A = a-type descendant
B = b-type descendant
C = c-type descendant

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?

Genetic "clocks" are relative dating mechanisms that can tell you that P happened before Q which happened before R, but not when they actually happened.

That IS what we seek here, isn't it? - the order. How much in common is A to C compared to how much in common is B to C?

Trying to understand the argument.


- xongsmith, 5.7d
This message is a reply to:
 Message 94 by RAZD, posted 06-13-2010 6:02 PM RAZD has acknowledged this reply

Replies to this message:
 Message 97 by Mr Jack, posted 06-15-2010 8:24 AM xongsmith has acknowledged this reply

    
Mr Jack
Member (Idle past 327 days)
Posts: 3475
From: Leicester, England
Joined: 07-14-2003


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.


This message is a reply to:
 Message 94 by RAZD, posted 06-13-2010 6:02 PM RAZD has acknowledged this reply

  
Mr Jack
Member (Idle past 327 days)
Posts: 3475
From: Leicester, England
Joined: 07-14-2003


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.


This message is a reply to:
 Message 95 by xongsmith, posted 06-14-2010 6:09 PM xongsmith has acknowledged this reply

Replies to this message:
 Message 98 by RAZD, posted 06-15-2010 11:39 PM Mr Jack has responded

  
RAZD
Member
Posts: 15818
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 1.8


Message 98 of 104 (565306)
06-15-2010 11:39 PM
Reply to: Message 97 by Mr Jack
06-15-2010 8:24 AM


Re: Cyanobacteria -- the ultimate "living fossil"?
               +----A1
|
+----|
| |
| +----A2
|
o----c----|
|
|
| +----C1
| |
+----|
|
+----C2

Enjoy

Edited by RAZD, : to match Mr Jack


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 97 by Mr Jack, posted 06-15-2010 8:24 AM Mr Jack has responded

Replies to this message:
 Message 99 by Mr Jack, posted 06-16-2010 4:39 AM RAZD has responded

  
Mr Jack
Member (Idle past 327 days)
Posts: 3475
From: Leicester, England
Joined: 07-14-2003


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.


This message is a reply to:
 Message 98 by RAZD, posted 06-15-2010 11:39 PM RAZD has responded

Replies to this message:
 Message 101 by RAZD, posted 06-16-2010 7:13 PM Mr Jack has responded

  
Blue Jay
Member (Idle past 5 days)
Posts: 2615
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(1)
Message 100 of 104 (565428)
06-16-2010 5:45 PM
Reply to: Message 60 by Europa
06-10-2010 6:15 PM


Hi, Europa.

I would like to input a little into this discussion: I hope you don't mind the intrusion.

Europa writes:

Do you guys honestly believe that the environment can remain similar for an organism for 200 million years?

Yes, they do. And, so, by the way, do I.

Perhaps we shouldn’t say, “the environment can remain similar”; it would be more accurate to say, ”the selection pressures caused by the environment can remain similar, even while the environment changes.”

This is because change is inevitable: we all think that all lineages and all environments will inevitably change over time. But, sometimes “change” means switching like for like.

For instance, an oak forest provides places for squirrels to live in and nuts for squirrels to eat. And, a pine forest also provides places for squirrels to live in and nuts for squirrels to eat. So, squirrels can probably make the evolutionary transition from oak habitats to pine habitats without altering their overall morphology all that much. So, there is no real pressure for squirrels to inherit major modifications to their body plan.

Dinosaurs came to watering holes in the Cretaceous in much the same way mammals come to watering holes today, and the adaptations of crocodilians for killing a drinking dinosaur work just as well on a drinking mammal. So, crocodilians can probably make the evolutionary transition from dinosaur-inhabited ecosystems to mammal-inhabited ecosystems without altering their overall morphology all that much. So, there is no real pressure for crocodilians to inherit major modifications to their body plan.

But, sometimes “change” means switching like for unlike.

Grass is an entirely different kind of plant from cycads and ferns. The mouthparts that were suitable for plucking and chewing cycads were not suitable for plucking and chewing grass. So, when grasses first began appearing, modifications to the mouthparts were required as part of the evolutionary transition to this new environment. These animals experience pressures that favor change.

Animals are less buoyant in air than in water. So, land-living animals have to support much more of their own weight than do water-living animals. So, modifications to the limbs and skeletons were required as part of the evolutionary transition between water and air environments. These animals experience pressures that favor change.

-----

Not all evolutionary situations are equivalent to one another, so it shouldn’t be a surprise that not all evolutionary situations result in the equivalent outcomes. It also shouldn’t be a surprise that not all evolutionary situations result in the same rate or the same extent of change.

Edited by Bluejay, : "...live in..."


-Bluejay (a.k.a. Mantis, Thylacosmilus)

Darwin loves you.


This message is a reply to:
 Message 60 by Europa, posted 06-10-2010 6:15 PM Europa has not yet responded

  
RAZD
Member
Posts: 15818
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 1.8


Message 101 of 104 (565438)
06-16-2010 7:13 PM
Reply to: Message 99 by Mr Jack
06-16-2010 4:39 AM


Re: Cyanobacteria -- the ultimate "living fossil"?
Hi Mr. Jack, you're still not seeing the whole concept quite right yet.

What we use to differentiate the A lineage from the C lineage are the differences we see now in the descendants.

... it could be that the entire branch of cyanobacteria that diverged into other life completely died out, ...

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.

Let's see if I can make it clearer:

               +----A'1
|
+----|
| |
A +----A'2
|
?----B----|
|
C +----C'1
| |
+----|
|
+----C'2

Where B is the basal species, responsible for the stromatolite formations, the earliest evidence we have of simple cell type life...

... which you validly point out does not necessarily have to be from what we would classify today as cyanobacteria ...

... and it diverges into two species A and C.

C has some traits in common with B that are not shared with A, and some new traits that are not shared with A or B. C'1 and C'2 are descendant species, with the traits that C does not share with A.

A has some traits in common with B that are not shared with C, and some new traits that are not shared with B or C. A'1 and A'2 are descendant species, with the traits that A does not share with C.

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.

To sensibly reject that interpretation you'd need strong evidence, which you don't have.

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.

To sensibly reject that interpretation you'd need strong evidence, which you don't have.

As opposed to no existing evidence for some made up ancestor, and ignoring evidence that B lived 3.5 billion years ago?

This issue is not about the formation of a genetic nested hereditary tree from the data that shows that the A lineage diverged from the C lineage very early in the diversification of life on earth.

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.

Enjoy.


we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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This message is a reply to:
 Message 99 by Mr Jack, posted 06-16-2010 4:39 AM Mr Jack has responded

Replies to this message:
 Message 102 by Mr Jack, posted 06-17-2010 4:33 AM RAZD has not yet responded

  
Mr Jack
Member (Idle past 327 days)
Posts: 3475
From: Leicester, England
Joined: 07-14-2003


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.


This message is a reply to:
 Message 101 by RAZD, posted 06-16-2010 7:13 PM RAZD has not yet responded

Replies to this message:
 Message 103 by barbara, posted 07-19-2010 3:56 AM Mr Jack has not yet responded

  
barbara
Member (Idle past 1205 days)
Posts: 167
Joined: 07-19-2010


Message 103 of 104 (568941)
07-19-2010 3:56 AM
Reply to: Message 102 by Mr Jack
06-17-2010 4:33 AM


Re: Cyanobacteria -- the ultimate "living fossil"?
Well if we did not spring forth from them then oxygen would not be considered anything beneficial to maintain. There is evidence that photosynthesis occurred without releasing oxygen as a waste product in other organisms. The fact is without oxygen there would be no need for higher complex life to emerge and evolve at all.

For the first 2 billions years these complex single celled organisms did just fine without us. The problem came in when the sun was growing stronger so they were either forced to learn to convert its energy which meant building an ozone layer to protect them in the process. This in turn affected their abundant supply of carbon that early earth had when it was forming the planet.

Creating a multicellular organism that allowed them to maintain the supply of chemical conversions that before naturally occurred from the planet was a solution to the problem.

The evidence of 2 HGT from two different species of single celled organisms confirms we were created by them. Another fact is that the mitochondria is a single celled organism with its own DNA that moved in our cells so it could control the whole respiration process tells you that they left nothing to chance. We are not an independent cell capable of living independently from single celled organisms.but they can be independent from us.

Another fact is without them in our digestive system we could not process the food efficiently to obtain all of the nutrients we need. Again they did not leave this important process up to us but manage it themselves inside of us.

Now if science is lying about this information that is currently being educated to the masses as a fact then science is no better than religions teaching us bullshit.

I explanation of natural selection and environment is responsible for evolution is weak in its explanation and it does not make any sense when you evaluate the whole picture from all areas of science.


This message is a reply to:
 Message 102 by Mr Jack, posted 06-17-2010 4:33 AM Mr Jack has not yet responded

Replies to this message:
 Message 104 by crashfrog, posted 07-19-2010 4:09 AM barbara has not yet responded

    
crashfrog
Inactive Member


Message 104 of 104 (568943)
07-19-2010 4:09 AM
Reply to: Message 103 by barbara
07-19-2010 3:56 AM


Re: Cyanobacteria -- the ultimate "living fossil"?
Well if we did not spring forth from them then oxygen would not be considered anything beneficial to maintain.

Considered by who? Maintained by who?

There is evidence that photosynthesis occurred without releasing oxygen as a waste product in other organisms.

There is indeed anaerobic phototrophy in some species, but photosynthesis specifically always produces gaseous oxygen. It's the inevitable result of using water as an electron donor in redox chemistry.

The problem came in when the sun was growing stronger so they were either forced to learn to convert its energy which meant building an ozone layer to protect them in the process.

When was the sun "growing stronger", and why? And what relevance would that have to organisms in the ocean, who are protected from UV radiation regardless of the presence or absence of ozone?

Creating a multicellular organism that allowed them to maintain the supply of chemical conversions that before naturally occurred from the planet was a solution to the problem.

Who thought this was a "problem" in need of a solution? Who "created" anything? What "chemical conversions" were not being created?

Barbara, you've created a narrative of the natural history of the Earth that is all but completely unmoored from fact, solely so that you can dispute the science of evolution.

But disputing evolution is going to have to occur from a basis of fact, not from fairy tales from pre-history.


This message is a reply to:
 Message 103 by barbara, posted 07-19-2010 3:56 AM barbara has not yet responded

  
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