alloytoo
Honorary Master
So you would say that those with the gene have been more successful than those without?
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Preadaptations
- Thread starter Phronesis
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So you would say that those with the gene have been more successful than those without?
Or genes were just lost along the way. Can't tell. Gene loss as well as co-option after selection are common as well.
alloytoo
Honorary Master
so you're saying the toolkit isn't universal?
Why would it be? Gene loss over time will make it impossible to determine. We do know that large parts of the hedgehog signaling system is distributed across all the domains of life. The most parsimonious explanation for that is that it had to be in the LUCA.
alloytoo
Honorary Master
If it's not universal then it's presumptious to assume it has been lost, why not assume it was never there?
That is not the most parsimonious explanation with regards to the LUCA.
alloytoo
Honorary Master
What do you mean?
If the same gene is present in euakryotes, bacteria and archaea, what is the most parsimonious explanation? That the same gene independently arose in different lineages, or that it was part of the genome of the last universal common ancestor and diverged from there. Now apply this to a whole set of genes and molecular structures that are shared across all the domains.
alloytoo
Honorary Master
I think you should try a different word to "Parsimonious.
Isn't very illuminative.
If we're assuming that LUCA had this toolkit, then we should be 100% certain that it's universal.
If it's not, can we positively identify deletions, or can we not posulate some other mechanism (Horizontal Gene Transfer) spread this gene around post LUCA?
We already know that retrovirus's can today sometimes become part of the Genome of complex creatures it seems precipitate to assume either independant development, or deletion events without considering HGT.
"Parsimonious" is fine. "least complex explanation for an observation", almost like Occam’s razor.
From wiki:
Well the genes are present in a diverse array of organisms across all the domains.
You can postulate other mechanisms. It would be near impossible to infer which mechanism happened when though and make phylogenetic assumptions less reliable. If you are making the case for HGT, you would need corroborating evidence for the situation you wish to prove. Otherwise the most parsimonious explanation will have to suffice.
alloytoo
Honorary Master
Actually it's not.
It's not used at all in the wiki article in the manner in which you use it.
The only use in the wiki article is:
The use of the word is abiguous in this context (oh the irony) "conservative" or "frugal" might well apply.
While the dictionary definition of Parsimony (Noun) includes
The definition of Parsimonious the adjective
This strongly suggests that your use of the word in this fashion is neither wide spread nor conventional.
Heh, I might refer you to the wiki quote above:
Without complete knowledge of that long a period ago, and the growing body of knowledge of HGT, it's hard to say with any certainty that it didn't happen.
The question would still be, why was LUCA, LUCA, and not something else?
Why was LUCA selected?
You are stuck on a definition again. "Parsimonious" is commonly used in scientific literature, especially when referring to cladistics and evolutionary trees.
From wiki again:
E.g.
Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida.
Trees of trees: an approach to comparing multiple alternative phylogenies.
Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle.
The infinite sites model of genome evolution.
Therefore, until you or anyone else provide actual evidence that HGT did occur for a particular case, the most parsimonious explanation needs to be accepted. This is how phylogenetic trees are drawn up; based on the most up to date information and parsimony. You are always advocating Occam's razor, well apply it here then. Don't introduce unnecessary variables without evidence when the simplest explanation will suffice. I am not saying HGT did not occur, just that evidence needs to be bought forth to challenge the most parsimonious explanation.
Let's see if you get this.
1) 4 organisms exist.
2) All 4 had a common ancestor
3) The 4 organisms have the following set of genes:
Organism a has the following set of genes: A, C, D, E, F, J, O
Organism b has the following set of genes: A, B, C, D, F, H, J, L, M, N, O
Organism c has the following set of genes: A, B, C, D, E, F, G, H, I, J, K, O
Organism d has the following set of genes: A, C, D, E, F, G, I, L, O
What set of genes would most likely be in the common ancestor of these organisms.
A) None?
B) Some (which one will satisfy the most parsimonious explanation?)
C) All?
From wiki again:
But if you are looking for the actual use of the word, look no further than scientific articles themselves and how the word relates to evolutionary phylogenetics (what we are discussing here).
E.g.
Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida.
Trees of trees: an approach to comparing multiple alternative phylogenies.
Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle.
The infinite sites model of genome evolution.
Therefore, until you or anyone else provide actual evidence that HGT did occur for a particular case, the most parsimonious explanation needs to be accepted. This is how phylogenetic trees are drawn up; based on the most up to date information and parsimony. You are always advocating Occam's razor, well apply it here then. Don't introduce unnecessary variables without evidence when the simplest explanation will suffice. I am not saying HGT did not occur, just that evidence needs to be bought forth to challenge the most parsimonious explanation.
Let's see if you get this.
1) 4 organisms exist.
2) All 4 had a common ancestor
3) The 4 organisms have the following set of genes:
Organism a has the following set of genes: A, C, D, E, F, J, O
Organism b has the following set of genes: A, B, C, D, F, H, J, L, M, N, O
Organism c has the following set of genes: A, B, C, D, E, F, G, H, I, J, K, O
Organism d has the following set of genes: A, C, D, E, F, G, I, L, O
What set of genes would most likely be in the common ancestor of these organisms.
A) None?
B) Some (which one will satisfy the most parsimonious explanation?)
C) All?
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alloytoo
Honorary Master
If "Parsimonious" were "commonly" used, it would have a sub-entry in at least some of the dictionaries, much like words "Intentionality" and "Evolution" have very specific sub entries related to very specific fields.
Parsimony has such a sub entry, "Parsimonious" does not.
If the usage you advocate were common it would pop up prominantly on google, it does not.
This suggests that the use of the word is either fringe, or ambiguous.
Certainly your usage of the word serves to discompose rather than elucidate.
While LUCA is the most facile explanation, it may be, as the wiki quote suggests, in the absence of information, simplistic.
Take the distribution of southern Hemisphere flightless birds for example, it was assumed that they shared a common anscestor and speciated due to continental drift. That was the simplest or Parsimonious (to make you happy)
explanation, it also turned out to be incorrect.
Orgel's Second Rule: Evolution is cleverer than you are.
Yet HGT does exist, in modern times HGT between vastly different clades have been observed.
None the less, the question remains did those Gene sequences give LUCA a competative edge over other Potential LUCA?
Just be sure to mention this to the authors and reviewers of hundreds of scientific peer-reviewed articles that use the word.
Exactly what I meant, use the most parsimonious explanation that explains the known data. Unless new data proves otherwise, Occam’s razor serve to arrive at the most parsimonious explanation.
You still have not shown that you get it. Here again (an example):
1) 4 organisms exist.
2) All 4 had a common ancestor
3) The 4 organisms have the following set of genes:
Organism a has the following set of genes: A, C, D, E, F, J, O
Organism b has the following set of genes: A, B, C, D, F, H, J, L, M, N, O
Organism c has the following set of genes: A, B, C, D, E, F, G, H, I, J, K, O
Organism d has the following set of genes: A, C, D, E, F, G, I, L, O
What set of genes would most likely be in the common ancestor of these organisms.
A) None?
B) Some (which one will satisfy the most parsimonious explanation?)
C) All?
Was it successful because it survived or did it survive because it was successful?
alloytoo
Honorary Master
Just be sure to mention this to the authors and reviewers of hundreds of scientific peer-reviewed articles that use the word.
Hundreds? You hyperlinked 4.
Nonetheless, as I pointed out earlier this isn't a science forum.
You know this silliness is bordering on trolling.
ACDFO are common genes
E & J could be common with erasures at bE & dJ
KMN are unique
a doesn't have B, G, H, I, L (or the Uniques)
Do b & c share a common ancestry with in J,B,H?
or Do c & d share E, G, I?
Either way how do b & d both get L
Erasures of bE, bG, bI, dJ, dB, dH and posibly cL?
Perhaps HGT might be a [-]more parsimonious[/-] simpler explanation. for L's distribution?
It is defined as successful because it survived, The question is WHY was it successful?
Then stop trying to say which definitions are scientific and which are not
.Species a-d are extant species, and it is not an evolutionary sequence a-d). They have a common ancestor, but are not related. Like Salmonella (bacteria), Lion, Fungus, and an archaeon.
You say it is succesful because it survived and then ask why it was succesful...
Uhm...
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alloytoo
Honorary Master
You say it is succesful because it survived and then ask why it was succesful...
Success=survival
Survival is not a reason, survival is an outcome.
Survival outcome is based on variables.
What variables favour survival outcome?
Success leads to survival or survival leads to success?
Is inbreeding a successful survival trick, or is survival a succesful inbreeding trick? Lots of examples of inbreeding in nature.
Natural selection does not select for function or against function, it just is right, it can't do anything.
So if there is nothing to select from (no function), it can't do any pruning. It is a useless idea without functionality. How does functionality arise? Self-organization?
Plenty of examples how functions arise with intent or self-organization. None through chance so far... Or can you give an example how a function arose through chance where cellular processes are not involved?
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alloytoo
Honorary Master
rwenzori
Honorary Master
This fellow was clearly pre-adapted for rapid change and survival:
http://mybroadband.co.za/vb/showthread.php?t=155308
http://mybroadband.co.za/vb/showthread.php?t=155308