How life evolves - our nucleii were once archeobacteria

[PB666]

http://www.biomedcentral.com/1741-7007/12/76

This paper basically argues that single lipid enclose archea can make blebs that would fuse to make the eucaryotic cell membrane and the outer bilayer of the nucleus. zduring the early process mitochondria were symbiotes that got captured and coated. The ER and golgi apparatus would have evolved later. A previous study has identified the Archea from which eucaryotes evolved , or a very close representative of an last common sncestor.

[KerikBalm]

I suppose its plausible, but I'm not going to label it as probable or the most likely explanation.

"A previous study has identified the Archea from which eucaryotes evolved , or a very close representative of an last common sncestor. "

Its absolutely not the Archea from which Eukaryotes evolved.

It does appear to be the closest relative to Eukaryotes though... that group would be the sister taxa of Eukaryotes.

[PB666]

Euchariotes are actually a polyploid, synsitia of archea and eubacteria. Therefore no archea can be our sole ancestor, thats a forgone, an with an MRCA in the 2 by time frame it is extemely unlikely we would see that transition. Actuallt this hypothesis seems likely. The mt precursor becomes an obligate sybiote of a larger archea, the effect is stronger the move enveloped the mt becomes. Its a likly progressed at that point as a division between the two membranes.

[KerikBalm]

Euchariotes are actually a polyploid, synsitia of archea and eubacteria.

Edited September 17, 2015 by KerikBalm

[PB666]

euKaryotes can be haploid, diploid, or poplyploid.

They are not synCYtial fusions of archea and eubacteria, as the mitos maintain their membranes. The are the result of symbiosis between an Archea and a Eubacteria.

mt are not separate from your cells, they are a part of your cell, your nucleus is separated from you by a bilayer, the mitochondria at its most basic level is dependent on the nucleus for enzymes required to reproduce, and the nucleus is dependent on the mitochondria for ATP, which it requires to create DNA. As an molecular paleontologist, there are X, Y and autosomes and mtDNA.

Nobody said it was... except maybe you. Obviously we are descendents of both an alpha proteobacteria and an Archea. When you figure in the lateral gene transfer that happens in microbes, you could even argue for additional ancestors.

Just to correct on something you said above as an example Wheat is hexaploid genome, originally there was a diploid wheat similar to Einkorn wheat, it then form a synsitia with another speltoid wheat to form Emmers wheat, and this then merge with Aegilops tauschii strangulatum to form bread wheat or hexaploid wheat, of course it also has chloroplast and mt. So its actually carrying 5 genomes.

The process of synsitia formation is not that unusual in nature. What makes this unusual is that the mitochondria and archea come from two separated kingdoms of life (as we see them)

I don't buy it. Nor have you given any reason for it to be likely relative to the established hypothesis. Many Alpha-proteobacteria are parasites of Eukaryotic cells, and actively invade Eukaryotic cells.

This is a discussion group no, no-one is forcing you to buy it. The critical issue here is that the key to intelligence was a transition from colony forming cells to differentiated cells, to do this without this merger would have been difficult, because the merger starts the process of specialization that then spreads from intracellular to extracellular. It is irrelevant whether bacteria are cell killers, viruses also kill cells, cells can invade and kill cells that is not a specialization of the phyla from which mitochondria arose. Second, have you ever seen a mitochondria from any species leave the cell that it was in and invade another cell? Even the mitochondria of a sperm cell are most often lost, almost never appear in the supsequent generation. Invading cells is not a trait of mitochondria.

What I am trying to say is this

Step 1. Archea

Step 2. Archea that has a cooperative relationship with bacteria on its surface (seen in the gut and soil bacteria). One bacteria produce one set of enzymes and perform one process and the other bacteria perform the other.

Step 3. Archea that then bleps membrane making certain relationships more efficient. Over time this evolves

Step 4. The membrane bleps surround the bacteria and form a very efficient cooperation, but for example cell division the symbiotes might be lost or the cell has less control

Step 5. the bleps surround and fuse, bringing the mt into the cell completely, the added consequence is that it has not created a nuclear bilayer that loops back on itself, the cellular plasma membrane and a two membrane mitochondrial membrane.

Step 6. This has to be done each generation until the machinary comes along allowing the plasma membrane to remain intact, and eventually the nucleus dissolves and reconstitutes itself during replication.

So if we are looking for life or life progressing toward advancement me might need to look for microbes that are in this transitional phase as well as other potential transitional phases. This study argues that phagocytosis and engulfation was not apart of the archea primordial species, if the bacteria entered cooperation was unlikely, but if the bacteria was blebbed over it could have been the result of a longer multigenerational cooperative strategy that finally became formalized in the unit of the cell.

[KerikBalm]

mt are not separate from your cells, they are a part of your cell, your nucleus is separated from you by a bilayer, the mitochondria at its most basic level is dependent on the nucleus for enzymes required to reproduce, and the nucleus is dependent on the mitochondria for ATP, which it requires to create DNA. As an molecular paleontologist, there are X, Y and autosomes and mtDNA.

#1) There is a physical seperation. Syncital means that the membranes would be fused, they are not. There are extensive internal boundries.

#2) The nucleus is not dependent upon the mitochondria for ATP, numerous Eukaryotic cells can survive without mitochondria. Have you ever heard of glycolysis? Anaerobic fermentation? (like what yeast, a eukaryote that is often in the haploid state, do)

#3) I'm really trying hard here not to make a personal comment in response to a personal comment about yourself.... but to address your last point, there are numerous species of Eukaryotes that entirely lack mtDNA.

https://en.wikipedia.org/wiki/Mitosome

Just to correct on something you said above as an example Wheat is hexaploid genome, originally there was a diploid wheat similar to Einkorn wheat, it then form a synsitia with another speltoid wheat to form Emmers wheat, and this then merge with Aegilops tauschii strangulatum to form bread wheat or hexaploid wheat, of course it also has chloroplast and mt. So its actually carrying 5 genomes.

Are you strawmanning me here?

How is that in any way correcting anything I said... quote that "something" that you claim I said...

The process of synsitia formation is not that unusual in nature. What makes this unusual is that the mitochondria and archea come from two separated kingdoms of life (as we see them)

You seem to be confusing syncitial (misspelled) and symbiosis here...

This is a discussion group no, no-one is forcing you to buy it.

And as a discussion group, points in opposition are allowed to be raised to it.

The critical issue here is that the key to intelligence was a transition from colony forming cells to differentiated cells, to do this without this merger would have been difficult,

There are multiple cases of specialization and multicellular structure formation in prokaryotes.

For example:

http://www.els.net/WileyCDA/ElsArticle/refId-a0000307.html

because the merger starts the process of specialization that then spreads from intracellular to extracellular.

Unsupported assertion. Contradicted by the example above

Second, have you ever seen a mitochondria from any species leave the cell that it was in and invade another cell?

I haven't seen it personally, but mitochondria transfer across cells is known, and can be artificially induced.

Have you ever even seen a mitocondria? I have. Do you think there are discrete mitochondria in your cells?

Please tell me how many mitochondria you see in the cell on the left, and how that mitochondria is supposed to invade another cell.

This question seems pretty asinine... like asking if you've ever seen a fish grow legs and walk on land, or rather a human grow flippers and gills and go live in the sea because our ancestors could.

Even the mitochondria of a sperm cell are most often lost, almost never appear in the supsequent generation. Invading cells is not a trait of mitochondria.

Not of mitochondria now, and there are active mechanisms to prevent it.

Using our lungs as a swim bladder is not a trait of humans... that doesn't mean that wasn't our lungs original purpose.

You are applying present day behavior of a highly evolved structure... to something 2 billion years ago that had a completely different selection pressure.

Also, cell parasitism is often not even invading... TB doesn't invade cells... it waits to get engulfed, and then survives and proliferates after being engulfed.

Do you dispute that mitochondria evolved from alpha proteobacteria?

Do you dispite that cell parasitism is widespread in alpha proteobacteria?

Do you dispute that if a trait is wide spread in a clade, it is was probably present in the LCA of that clade?

What I am trying to say is this

Step 1. Archea

Step 2. Archea that has a cooperative relationship with bacteria on its surface (seen in the gut and soil bacteria). One bacteria produce one set of enzymes and perform one process and the other bacteria perform the other.

Step 3. Archea that then bleps membrane making certain relationships more efficient. Over time this evolves

Step 4. The membrane bleps surround the bacteria and form a very efficient cooperation, but for example cell division the symbiotes might be lost or the cell has less control

Step 5. the bleps surround and fuse, bringing the mt into the cell completely, the added consequence is that it has not created a nuclear bilayer that loops back on itself, the cellular plasma membrane and a two membrane mitochondrial membrane.

Step 6. This has to be done each generation until the machinary comes along allowing the plasma membrane to remain intact, and eventually the nucleus dissolves and reconstitutes itself during replication.

I understand their model, I just don't think the evidence supports it.

The idea that the plasma membrane formed as an outer membrane/extension of the nuclear membrane instead of the nuclear membrane forming as an in......tion of the plasma membrane is interesting however.

I don't think the evidence supports the incorporation of mitochondria in this fashion. I'm still going to favor the endocytosis/invasion pathway given what happened with algae and cyanobacteria, the conserved endocytosis mechanisms, and that cell parasitism is widespread in alpha proteobacteria.

Its interesting to think that maybe endocytosis initially involved growing protrusions, rather than forming in......tions... but the current endocytosis machinery seems incompatible with that... and requires that there was an original system that was lost or modified so much that it is unrecongnizable.

This hypothesis just seems to be more complicated and insert more speculative steps that we have no evidence for.

So if we are looking for life or life progressing toward advancement me might need to look for microbes that are in this transitional phase as well as other potential transitional phases. This study argues that phagocytosis and engulfation was not apart of the archea primordial species, if the bacteria entered cooperation was unlikely, but if the bacteria was blebbed over it could have been the result of a longer multigenerational cooperative strategy that finally became formalized in the unit of the cell.

Yes, but I don't see how it explains the observations better than the current hypothesis.

Its an interesting idea to keep in mind for the next new observations, but I'm not about to go telling people that this is how it probably happened.

Edited September 17, 2015 by KerikBalm
spelling

[KSK]

I understand their model, I just don't think the evidence supports it.

The idea that the plasma membrane formed as an outer membrane/extension of the nuclear membrane instead of the nuclear membrane forming as an in......tion of the plasma membrane is interesting however.

I don't think the evidence supports the incorporation of mitochondria in this fashion. I'm still going to favor the endocytosis/invasion pathway given what happened with algae and cyanobacteria, the conserved endocytosis mechanisms, and that cell parsitism is widespread in alpha proteobacteria.

Its interesting to think that maybe endocytosis intiially involved growing protrusions, rather than foring in......tions... but the current endocytosis machinery seems incompatible with that... and requires that there was an original system that was lost or modified so much that it is unrecongnizable.

A little off-topic but I'm going to try an experiment here:

invagi-nation

Yeah that's what I hoped. I think it's sad when the 'profanity' filter blocks out the anatomically correct term as a 'rude' word and mangles any words including it. I guess we could call them in-front-bottom-inations.

Edited September 17, 2015 by KSK

[KerikBalm]

ah yes, auto censor, because this is the internet and even on the science forums, we can't trust people ot be mature.... *sigh*

Also, as an addon to the nucleus = original cell model.

If that were the case, then during cell division, I would expect to see the nucleus divide like a cell does, and then cleave the cytoplasm down the middle, like the archea with the outer membrane in one of the cited papers (of the paper in the original post).. or how bacteria in general with outer membranes divide.

Instead... the nucleus... disappears completely... and we have cells with no nucleus what so ever... and then a nucleus is later formed de novo.

Keeping in mind that mitochondria (which are basically a very simple cell within a complex cell) cannot form de novo within a cell... it seems amazing that a "nuclear cell" could form.

- Not impossible... but it seems unlikely to me that this would happen if the nucleus was in fact the "original" extent of the cell.

Combined with the reasons I already gave (widespread endocytosis, clear example of an similar symbiosis occuring after the nucleus formed[chloroplasts], mitochondria being most closely related to a parasitic clade of alpha proteobacteria, etc.)... I'm really not in favor of this hypothesis.

Edit again:

Also, in this model, the outer mitochondria membrane would be the same as the outer nuclear membrane (the nuclear membrane is a double membrane... each membrane is a lipid bilayer, so the whole thing is not really a bilayer, more of a quad-layer) initially.

To my knowledge, there is not a single species in which this is observed, nor are there any similarities that would suggest it was this way in the past.

Edited September 17, 2015 by KerikBalm

[PB666]

So the basic arguement here concerns one person who states that we can apply variant notions of life to xenobiotic studies and another person who is exactly focused on a single notion of how life evolved. I could respond to all the comments creating a wall of words, I will respond to a few things, but make the statement that you cant make a five course meal starting from concrete. Either your starting materials have got to be flexible in their design or your craft will be nothing but structurally undefined aggregate. (Without using personal comments).

#1) There is a physical seperation. Syncital means that the membranes would be fused, they are not. There are extensive internal boundries.

#1a. Yes, which serves a function, that function is to keep the hydroxyl free radicals away from the DNA of both cells. So there is a grand reasoning for not incorperating mtDNA into the genome for its primary purpose of generating ATP and NADPH. Functional preservation of an ancestral trait.

#1b. Yes, by separating the genomes (mostly, many mtDNA genes are now encoded by the genome), the mt are free to divide, so for example an sperm cell may have x number of mt and a muscle may have 1000x mtDNA per haploid genome. IOW this allows cells to differentiate DNA copy number allowing for oxygen requiring cells.

#2) The nucleus is not dependent upon the mitochondria for ATP, numerous Eukaryotic cells can survive without mitochondria. Have you ever heard of glycolysis? Anaerobic fermentation? (like what yeast, a eukaryote that is often in the haploid state, do)

This is a very good reply. But we need to focus on the variants of the process. There are eucaryotic cells that have adapted a wide variety of processes including glycolysis. Certain benthic worms use another organelle to process other sugars for energy. There are a wide variety energy extraction processes, and certainly the evolution of cyanobacterium influenced the course of life on earth due to the great oxygenation event. These other processes can also be seen as evolutionary variants, including cells that loose mitochondria. I can refer to the fact the red blood cells also loose their nucleus, this is another variant. So which is more important the nucleaus or the mitochondria, or maybe its a bad question, maybe the question should be how has selection evolved to force structure function changes.

#3).... but to address your last point, there are numerous species of Eukaryotes that entirely lack mtDNA.

https://en.wikipedia.org/wiki/Mitosome

And there are some that for the most part don't use their mtDNA, as might have been the case when mt were encorperated into cells. The point of forming a cell is that it facilitated life, more than a billion years ago, and since then have you seen a truely single cell procaryote come forth that is progressing in the direction of multiorgan life, Even an annelid like work would suffice as evident. No..So you are essentially digging around for exceptions and claiming they are the rule.

The rest of the post is cut short because of the level of diatribe. The point is that fundamentally we don't know and can't be clear, you are denigrating the authors (and me), but as a matter of point you are showing a concretized point of view. This is particularly relevant for study of xenobiota since we are not likely going to find ants, nematodes or other forms of life. The mostly forms of life we will find are in the transitional or pretransitional phase. Its not about, or has nothing to do with elaborate images of what our minute instances of life look like. Terraforming on any scale would require a knowledge of the basics, you can easily eradicate all higher lifeforms on a planet, but getting rid of the basal forms and early transitional forms would be the hardest. And if you do not understand them and how they might have evolved then controlling their behavior will be difficult.

I should point out classically the hardest diseases to fight (such as malaria, chaga's disease, etc) are organisms more similar to humans than bacteria or viruses. Ergo seeing the variants is more important than wishing for a foregone conclusion. Other than that I like their hypothesis, its kind of neat, and new hypothesis like this always cause hypish controversy which has been the lingua franca of science for centuries, no problem with that either and more than that it draws people out of their little comfort zones and makes them think........ continue diatribe.

- - - Updated - - -

ah yes, auto censor, because this is the internet and even on the science forums, we can't trust people ot be mature.... *sigh*

Trust me, you'll like moderation when its not present.

[KerikBalm]

So the basic arguement here concerns one person who states that we can apply variant notions of life to xenobiotic studies and another person who is exactly focused on a single notion of how life evolved.

This is the first time any mention of xenobiotic studies has occured on this thread.

The original post was about a notion of how Eukaryotes evolved, and I was staying on topic.

I could respond to all the comments creating a wall of words, I will respond to a few things, but make the statement that you cant make a five course meal starting from concrete. Either your starting materials have got to be flexible in their design or your craft will be nothing but structurally undefined aggregate. (Without using personal comments).

... Or you could actually address the various points raised

... or you could just go on random non-sequiturs while trying to seem smart...

I see you're going with the last one

#1a. Yes, which serves a function, that function is to keep the hydroxyl free radicals away from the DNA of both cells. So there is a grand reasoning for not incorperating mtDNA into the genome for its primary purpose of generating ATP and NADPH. Functional preservation of an ancestral trait.

#1b. Yes, by separating the genomes (mostly, many mtDNA genes are now encoded by the genome), the mt are free to divide, so for example an sperm cell may have x number of mt and a muscle may have 1000x mtDNA per haploid genome. IOW this allows cells to differentiate DNA copy number allowing for oxygen requiring cells.

Congratualtions on sticking with the random non sequiturs.

Nothing in this reply supports or is related to your assertion that mitochondria are syncitial with the rest of the cell (If you meant something else, please specify, I am not trying to strawman you).

This is a very good reply. But we need to focus on the variants of the process. There are eucaryotic cells that have adapted a wide variety of processes including glycolysis. Certain benthic worms use another organelle to process other sugars for energy. There are a wide variety energy extraction processes, and certainly the evolution of cyanobacterium influenced the course of life on earth due to the great oxygenation event. These other processes can also be seen as evolutionary variants, including cells that loose mitochondria. I can refer to the fact the red blood cells also loose their nucleus, this is another variant. So which is more important the nucleaus or the mitochondria, or maybe its a bad question, maybe the question should be how has selection evolved to force structure function changes.

And this is not.

You made some statements. I showed they were false.

Then you just threw out some random factoids that have nothing to do with the subject at hand.

The rest of the post is cut short because of the level of diatribe. The point is that fundamentally we don't know and can't be clear, you are denigrating the authors (and me), but as a matter of point you are showing a concretized point of view.

I am trying to have a rational discussion.

I said the author's supposition was plausible.

I said "Its an interesting idea to keep in mind for the next new observations, but I'm not about to go telling people that this is how it probably happened."

And yet I'm close minded?

I'm just being rational, and not just accepting and promoting a new view because it is new.

This is particularly relevant for study of xenobiota

Ok.. so if you wanted to talk about how things might happen on another world you should have said so.

Your last post is the first post that said anything about Xeno anything - err well I see at the very end of post 5 something that could be interpreted that way, but I missed it on my intial reading.

Anyway, as I already said... its plausible, but given the evidence, I doubt it happened.

Reply to the actual arguments rather than going on random non-sequiturs (often it seems to have an air of condescension too, which rubbed me the wrong way... like replying to my post with "as an molecular paleontologist" and then stating stuff as if I'm displaying ignorance on the subject), don't strawman me (still waiting for you to quote that "something said" that needed correcting), and you won't get any diatribe.

Other than that I like their hypothesis, its kind of neat, and new hypothesis like this always cause hypish controversy which has been the lingua franca of science for centuries, no problem with that either and more than that it draws people out of their little comfort zones and makes them think........ continue diatribe.

Yes, and I never said it wasn't. I said:

"The idea that the plasma membrane formed as an outer membrane/extension of the nuclear membrane instead of the nuclear membrane forming as an in......tion of the plasma membrane is interesting"

"Its an interesting idea to keep in mind for the next new observations"

"I suppose its plausible"

Edited September 17, 2015 by KerikBalm

[PB666]

This is the first time any mention of xenobiotic studies has occured on this thread.

The original post was about a notion of how Eukaryotes evolved, and I was staying on topic.

PB666 about 6 posts back: So if we are looking for life or life progressing toward advancement me might need to look for microbes that are in this transitional phase as well as other potential transitional phases.

I did not say anything about earth in this sentence, it refered to life anywhere

Enough said.

http://www.ncbi.nlm.nih.gov/pubmed/26187720

Edited September 17, 2015 by PB666

[KerikBalm]

PB666 about 6 posts back: So if we are looking for life or life progressing toward advancement me might need to look for microbes that are in this transitional phase as well as other potential transitional phases.

So... the last sentence of a long post, 2 out of 3 of my replies to you before your post about "the basic arguement here concerns one person who states that we can apply variant notions of life to xenobiotic studies" were before that statement.

If that was your basic argument, you should have stated it much sooner, and much more explicitely, because I simply did not get that impression from a thread with the claim "our nucleii were once archeobacteria"

I naturally thought the discussion would be about that claim.

It seems you don't want to discuss it, but instead want to discuss how life on another world might evolve a complex cell.

When I read "So if we are looking for life or life progressing toward advancement me might need to look for microbes that are in this transitional phase as well as other potential transitional phases." that after a post exclusively about life on earth, I thought you were talking about Earthly forms that may display primitive traits/be similar to the transitional form.

I thought it was related to your statement earlier: "Therefore no archea can be our sole ancestor, thats a forgone, an with an MRCA in the 2 by time frame it is extemely unlikely we would see that transition."

Specifying "other worlds" or "alien" or using the prefix "Xeno" would be very helpful in a discussion that had up until that point been about Earth life and hypothetical past Earth life.

Edited September 17, 2015 by KerikBalm

[PB666]

So... the last sentence of a long post, 2 out of 3 of my replies to you before your post about "the basic arguement here concerns one person who states that we can apply variant notions of life to xenobiotic studies" were before that statement.

If that was your basic argument, you should have stated it much sooner, and much more explicitely, because I simply did not get that impression from a thread with the claim "our nucleii were once archeobacteria"

I naturally thought the discussion would be about that claim.

It seems you don't want to discuss it, but instead want to discuss how life on another world might evolve a complex cell.

When I read "So if we are looking for life or life progressing toward advancement me might need to look for microbes that are in this transitional phase as well as other potential transitional phases." that after a post exclusively about life on earth, I thought you were talking about Earthly forms that may display primitive traits/be similar to the transitional form.

I thought it was related to your statement earlier: "Therefore no archea can be our sole ancestor, thats a forgone, an with an MRCA in the 2 by time frame it is extemely unlikely we would see that transition."

Specifying "other worlds" or "alien" or using the prefix "Xeno" would be very helpful in a discussion that had up until that point been about Earth life and hypothetical past Earth life.

The archea subclass resposible for eucaryotic nucleus was recently detained in the journal Science, and of course the mt carry their own genome. But i must protest that the variants in metabolism, mt, and nucleus are statistically important in establishing deviant ranges. Adding to this the idea the mt interact within the cell, combined these two phenomena create a multidimensional variation that allows not wide single cellular adaptations, but multicellular specialization.

From a statistical POV one has to broaden the perspective even farther to deal with black swans, those things that exist, but we haven't identified yet, such as true branches from the transitional state. But also dead-ends from the transitional state that go unobserved. In our reality they are unimportant, as with pretty much the transitional state in general. However the question could be asked how long did eucaryotic transition take place, were their other versions that never ended in our version of a eucaryote, or wiped out by our version of the cell.

So the hypotheticals go in the blackbox, insert a broadening scope, and output plausibilities. Then classify exobiota according to the possibilities.

I have a critique of the article, you pointed out several weaknesses, but the biggest two weaknesses go unexplained.

The one problem, inva-gination is explained as a later evolutionary event. But there are two problems.

1. if the cell evolved from the nucleus, then breakup of the nuclear membrane for replication was not part of cell division, this would have to have evolved over a long period of time after ward, so once the membranes fused how exactly does the cell divide. Once the nuclear membrane is torn down to replicate what is the evolutionary pressure to rebuild. It seems very odd that evolution would append the nucleus, then destroy it and rejuvenate it. This would have been a very risky process.

2. The endoplasmic reticulum originates from the nuclear membrane but it is not a blebbing from th inner layer, but from the outer layer, an the golgi apparatus is the exact opposite process that the paper describes.

These problems offer up th potential for other explanations.

[KerikBalm]

The archea subclass resposible for eucaryotic nucleus was recently detained in the journal Science, and of course the mt carry their own genome. But i must protest that the variants in metabolism, mt, and nucleus are statistically important in establishing deviant ranges. Adding to this the idea the mt interact within the cell, combined these two phenomena create a multidimensional variation that allows not wide single cellular adaptations, but multicellular specialization.

From a statistical POV one has to broaden the perspective even farther to deal with black swans, those things that exist, but we haven't identified yet, such as true branches from the transitional state. But also dead-ends from the transitional state that go unobserved. In our reality they are unimportant, as with pretty much the transitional state in general. However the question could be asked how long did eucaryotic transition take place, were their other versions that never ended in our version of a eucaryote, or wiped out by our version of the cell.

What are you even responding to here?

Btw

"The archea subclass resposible for eucaryotic nucleus was recently detained in the journal Science, "

No... the archea that is phylogentically closest to Eukaryotes was recently described.

"But i must protest that the variants in metabolism, mt, and nucleus are statistically important in establishing deviant ranges"

What are you even protesting about? what are you responding to?

"From a statistical POV one has to broaden the perspective even farther to deal with black swans, those things that exist, but we haven't identified yet,"

What are you talking about?

You quote me, but then what follows doesn't seem to apply to what I said...

"However the question could be asked how long did eucaryotic transition take place, were their other versions that never ended in our version of a eucaryote, or wiped out by our version of the cell."

Yea... I imagine there were stem Eukaryotes that had a nucleus, but hadn't yet taken up mitochondria. I guess none of them made it

All Eukaryotes today have mitochondria, or came from ancestors that did (those that lack mitochondria have a secondary loss of mitochondria, their primitive state was + mitochondria).

If we found such a stem Eukaryotes or "transitional form", this theory/hypothesis would be thoroughly disproven, rather than just plausible but not convincing/probable.

[PB666]

What are you even responding to here?

Btw

"The archea subclass resposible for eucaryotic nucleus was recently detained in the journal Science, "

No... the archea that is phylogentically closest to Eukaryotes was recently described.

I take that if said the dinosaur subclass resposible for birds ......... this would also upset you? try not to be too ........

"But i must protest that the variants in metabolism, mt, and nucleus are statistically important in establishing deviant ranges"

What are you even protesting about? what are you responding to?

"From a statistical POV one has to broaden the perspective even farther to deal with black swans, those things that exist, but we haven't identified yet,"

What are you talking about?

You quote me, but then what follows doesn't seem to apply to what I said...

I am protesting the desire to suggest that the final path taken is reflective of all paths or plausible paths. I want to broaden the arguement so far away from this that we are also looking at paths potentially taken say from other archean or even other bacteria. Without getting to absurb argument.

However the question could be asked how long did eucaryotic transition take place, were their other versions that never ended in our version of a eucaryote, or wiped out by our version of the cell."

Yea... I imagine there were stem Eukaryotes that had a nucleus, but hadn't yet taken up mitochondria. I guess none of them made it

All Eukaryotes today have mitochondria, or came from ancestors that did (those that lack mitochondria have a secondary loss of mitochondria, their primitive state was + mitochondria).

If we found such a stem Eukaryotes or "transitional form", this theory/hypothesis would be thoroughly disproven, rather than just plausible but not convincing/probable.

Why do you need to disprove one hypothesis over another. Science is what expands the boundaries of science, not contracting it. One professor at my school once confided that every time she excluded a regulatory patway in one tissue, some other researcher would find that pathway in another tissue. 30 years ago scientist were convinced that only proteins could be a enzyme. Such fixations are not neccesary. Sure some pathways are water tight, overall evolution is a very leaky business. I personally don't want to live in exclusive landscape anymore, one tends to get buried with ones fixtures in their epitath.

Red blood cells also loose their nucleus. But I think the issue is more abstract, because there might have been many different types of inclusion, plants are exemptlary. But you could've had cells in the intermediate phase picking biotes/biochemistry like picking candy from a vending machine, later processes of assimilation bringing their unique genes into the genome and washing the cell of contents.

An example of a nearly absurb argument would be the nitrogen fixing cyts of certain cyanobacterium. These particular units have a biochemistry that is highly toxic to other forms of life. Nitrogen fixation in nature is classically left to certain procaryotes. In fact if we look at all life there is a something somewhere that can take advantage of just about any source of potential chemical energy. wouldn've it been interesting if some early singke cell plants has variants of the cyts that was poisonous but a lipid bilayer protected the host, and the cyst were exchanged between different cells, so that cells in a psuedo colony had the oppurtunity to pick up bioavailable nitrogen before they got intoxicated.

In the papers model this is possible because the cell membrane would be drafted each generation, a procaryotes do have forms of DNA transfers. In this case instead of exchanging nuclear DNA they exchange cynobacteria, robbing the cyanos environment of nitrogen and forcing them to fix. When the cell gets too affected it seeks out a mate that then takes the cyst and leaves the nitrogen enriched cyanos behind. The cyst would then grow cyanos in the recipient cell. The donor cell would slowly degrade the cyanos by dilution in daughter cells or through apoptosis.

But this does not explore other possibilities, because the subclass of archea can also be considered a fixation of the argument, we could also look at cells that had pairing with markedly differnent types of archea whose dominat status dependent on the environment, sort of like a binary star system.

Edited September 19, 2015 by PB666

[KerikBalm]

I take that if said the dinosaur subclass resposible for birds ......... this would also upset you? try not to be too ........

I'm just being technical... its in my nature. I'm like this, I nitpick, I don't mean offense, FYI, I'm hoping to be a patent attorney after finishing my PhD, so the use of technically correct langugage should become even more important to me in the future

#1) This isn't really analagous though, because birds arose from a group within dinosaurs, whereas Eukaryotes did no arise from within the species recently described in Science. Eukaryotes and that clade are sister taxa. Birds are a subset of dinosaurs, there is a distinction

#2) Implicit in the statement is support for this nucleus = original cell idea. Otherwise you'd probably have said "resposible for eucaryotic cell" instead of "resposible for eucaryotic nucleus"

I am protesting the desire to suggest that the final path taken is reflective of all paths or plausible paths. I want to broaden the arguement so far away from this that we are also looking at paths potentially taken say from other archean or even other bacteria. Without getting to absurb argument.

Ok, well, I think we can follow two paths at once.

#1) What happened in our history

and

#2) What might happen if we "turned back the clock" or on another world.

Why do you need to disprove one hypothesis over another. Science is what expands the boundaries of science.

Science is what explains the natural world/observation (your statement is a bit of circular reasoning).

Why disprove something? Because science is about answering questions. Its all about testing a hypothesis.

In the process of testing, you may disprove.

If you repeatedly test and fail to disprove, and it generates predictions which you can then confirm... you at least have a model with good explanatory power.

I'd like to explain how it happened here on Earth, wouldn't you?

But to your broader question, I don't think we need to restrict ourselves to "Eukaryote"-like cells.

As I said in one of my Early replies, there are some prokaryotes that form macroscopic multicellular structures, with differentiated cells.

There is cell-cell signalling among prokaryotes.

I think if all Eukaryotes were to be wiped out, we'd see mutlicellular life come back pretty fast, maybe even before a nucleus like structure, or endosymbiosis.

Maybe the Ediacaran biotoa was all prokaryote?

I'd really like to know more about the Ediacaran biota... we know almost nothing of them.

Kimberella seems to have been a stem-mollusc, so they were probably Eukaryotes, and the timing is right, but we can't be sure.

They probably were...

Notice I dont speak in absolutes... I'm open to many possibilities, but I do know certain possibilities are probably not what actually happened.

[MinimumSky5]

As an molecular paleontologist, there are X, Y and autosomes and mtDNA.

Molecular paeleontilogists have trouble studying DNA, as DNA is a quite unstable molecule that decays after a few thousand years (in very good conditions

conditions). This nucleus creating event likely happened about 1.5 to 2 billion years ago, so how can you study DNA locked inside rocks of that age? If you meant to refer to recent organisms, a better term would be molecular biologist, or molecular paeleobiologist at a push. Also, it's generally accepted that sexual reproduction evolved about 800 - 700 million years ago, so the X and Y chromosomes aren't really important in this discussion.

[PB666]

If you repeatedly test and fail to disprove, and it generates predictions which you can then confirm... you at least have a model with good explanatory power.

I'd like to explain how it happened here on Earth, wouldn't you?

Funny story my advisor called me concretized, that was because he was defending his animal model, as it turned out his model is sort of one of a kind. So maybe I wasn't too concretized. But from this point of view I would be, be cause what i discovered in that structures that could assemble into billion molecular weight protein complex complete with an internal scaffold of support proteins. See that was science, because it broke the mold of what other people were studying. Alot of what people call science is actually systematics. If you are in biotechnology patents, alot of the proteins you may see, the first charcterizations, basically showing the world this new variant exists and its different, these things flow through my hands everyday, but its more akin to stystematics and molecular clonology than science. I see so many of the same kind of manuscript. (x does this and has been done, y does that and has been studied, here we make XY and looky its really potent) All they are doing is taking something that we've already known about purifying it away from toxins and inhibitors, maybe tweeking it to be more stable, it prolly already works we'll and in many cases making it easier to produce and purify. Aftervthey get this they head to the uni patent lawyers. Science really is not abou knowledge, its about pushing the boumdaries into the unknown. Occasionally while you are doing the technocloning stuff something really goes wrong and a truely new novelty is discovered.

For it to work, the hypothesi, you really have to have an annoying question, like why does this thing work. You show it works this way overhere, then tomorrow someone shows it works another way overthere. Its all right.

But to your broader question, I don't think we need to restrict ourselves to "Eukaryote"-like cells.

As I said in one of my Early replies, there are some prokaryotes that form macroscopic multicellular structures, with differentiated cells.

There is cell-cell signalling among prokaryotes.

I think if all Eukaryotes were to be wiped out, we'd see mutlicellular life come back pretty fast, maybe even before a nucleus like structure, or endosymbiosis.

Maybe the Ediacaran biotoa was all prokaryote?

Yep, someone suggested they might be after large marine unicellulars were discovered, they certainly are mysterious. The stromalites are procaryotic. But there is something different about eucaryotes. You might find stromalite like creatues on other worlds. The question is do we know enough about our ancient earth that we would be able to recognize it, and how would we respond.

[KerikBalm]

Nope, I'm not into patents yet, still finishing my PhD on a class of proteins involved in RNA regulation in mitochondria.

Our lab recently described new RNA processing structures within mitochondria, hopefully by the end of the year I'll have 2 first authors and a 2nd author on a review...

So yea... you don't need to tell me about the basics of mitochondria as in earlier posts, and it is new, and it is science.

We have many hypothesese on what these structures are doing, and what these proteins are doing, and we need to test them. Its not enough to say it could be this or it could be that (though that is done as well).

[PB666]

Nope, I'm not into patents yet, still finishing my PhD on a class of proteins involved in RNA regulation in mitochondria.

Our lab recently described new RNA processing structures within mitochondria, hopefully by the end of the year I'll have 2 first authors and a 2nd author on a review...

So yea... you don't need to tell me about the basics of mitochondria as in earlier posts, and it is new, and it is science.

We have many hypothesese on what these structures are doing, and what these proteins are doing, and we need to test them. Its not enough to say it could be this or it could be that (though that is done as well).

I used to play with mtDNA systematics, I have sonewhere (when i get my linux machine built) an excel sheet with all the known eutherians mt DNA aligned. I have classifed every site within mtDNA according to its rate of evolution, every five years or so i reallign then with the new DNA so that the branch points. This is so when they discover a new human mtDNA group or new hominid mtDNA i can immediately guess when it branch. It was originally aligned with clustalw and then converted with visual basic to abd excel sheet. Its got the little genes marked off according to tRNA genes and the enzymes. I did this because there was a debate about a decade ago whether the elevated rate in humans was due to purifying selection or directional adaptation. It turns out some specific lines in humans show an extensive series of mutations that are very uncommon in other eutherians. one of the branches dated based on the slowest evolving sites is around 2mya, the population that Tishkoff says is under neutral selection dates to around 250ky. This evolving mtDNA population appears to have traveled from africa to india to the west pacific rim to alaska and to south america. Each time it migrated to a new different temperature habitat certain genes tended to change. So the general rule of purifying selection appears not to be true in specific examples of adaptive selection. These mutations allow me to dice out in much older branches which mutations are indicative of clock acceleration and which are indicative neutral drift. I had to give it up a few years ago because of the limitations of my health and the machine i was using, but with the new machine, updated system i can get back to it. When it comes to evolution in mammals partularly durind embryogenesis and early development I had been well read on mtDNA. Things like the prospect of recombiation or paternal inheritance.

I actually tried to draft mtDNA from other reptiles, the branch times are pretty hideous and the differential evolution is hard to resolve at the genomic level. My real interest in the project however has passed since more interested in functional demes than mtDNA and the new ancient genome sequences have managed to address many of the concerns the locus i work on evolves oddly in humans, if i can get more alligned DNA from the desinovan group I actually can begin to evaluate some of the selection coefficients in that locus, I have 2 64gb memory pens full of desinovan DNA overlaps but no computer yet capable of processing it, hopefully withbthe linux on a quad core I will be able to covert a VBA to C and finally parse out the region of chromosome 6 I am interested in. Not doing anything now because stuck on hideous Ipad for 2 weeks.

The point I was making is that when you get into the patent stuff, the stuff the scientist are doing now for medical science and food industry its alot of processing, not very elaborate stuff, it does get published, I should know, but much of it is trivial. Variant X does this and Y does that. the comment is not about your Ph.D. work at all, when you comb the literature for patent research you will see a horriffic amount of trivial studies that are simply sticking a flag on the mun.

[KerikBalm]

Yea, but its better pay, more stable work, and I don't have to be in a lab working with radioactive P32 and S35, and toxic chemicals like Ethidium Bromide, Chloroform, formaldyhyde, etc.

Nor do I need to work with Lentiviruses...

So it seems to have many advantages...

[PB666]

Yea, but its better pay, more stable work, and I don't have to be in a lab working with radioactive P32 and S35, and toxic chemicals like Ethidium Bromide, Chloroform, formaldyhyde, etc.

Nor do I need to work with Lentiviruses...

So it seems to have many advantages...

EtBr no problem

Chloroform/ DCM worked with, causes liver disfunction and anxiety. Long term effects are like being doses up on caffiene, takes a week or two to wear off in some individuals, not worse than the long term affects of tylonol.

Formaldehyde is bad stuff.

Radionucleotides i don't worry about, its the regulatory thats the major hassle. And S35 is a big cleanup issue because you are almost always using it in a biological uptake assay, its best to cover the floor os the work area in absorbant paper when you decide to pull the SDS-PAGE out of the EPA, buy a disposable dish pan close and lock the door.

If you increase the toxicity of formaledhyde a million fold, then you are in the range of the bad guys i deal with, fortunately im old enough now i can delegate, i write the protocols and enforce, when they listen to me, lol.

Viruses of course are BSAs, so you are either immunized, or pay the price. We used to have a BSL3 next door to us, and i was the floor fire warden the old protocol was that i had to flush folks out of the rooms, now all the rooms are strobed and alarmed.

The regulatory stuff is the major reason I want out, its disproportionate toward science now, particularly if the Inst. takes NIH or NSF funding. Much of the time is spend dealing with unneccesary checks. The work is stable the pay is low.

[KerikBalm]

EtBr is a mutagen and suspected carcinogen... and Latex gloves aren't enough.

Even Hoecst stain isn't great.

Nor is trizol... or BME.

Pretty much everything in the lab is something you don't want to have on your skin... and I don't even have a desk in another room.

And in the lab where I work with P32 and S35, some people use C14... which lasts forever (from the practical viewpoint of the human lifespan), and they use it in pyruvate uptake assays, where it can ultimately be converted to CO2... sure they have something that is supposed to absorb the CO2 released...

A while back one of the CO2 lines to a cell incubator came off... if nobody had been in the room when it happened, the room could have filled with CO2, and the next one to come in could have shut the door behind them and passed out...

I'd rather just avoid the whole affair of working in a lab + the frustration of experiments that don't work.

[PB666]

EtBr is a mutagen and suspected carcinogen... and Latex gloves aren't enough.

Even Hoecst stain isn't great.

Nor is trizol... or BME.

Latex isn't good for anything organic chemistry. Using latex with chloroform is one step removed from self-injecting latex polypetides. EtBr is a generational hazard. If you are older than me your lab would have EtBR everywher, your gels go into the trash and the cleaning people handle them, you handle anywhere, never seen anyone hurt by it. If you are my generation, you have the gels in a well vented room, use and change the diapers frequently you keep the gel area clean and you dispose of them in large plastic bags and send to Env Safety. If you are younger than my generation you freak out at the site of EtBr bottle, you move all the gel equipment into the hood and you call env safety if you have the slightest spill of EtBr (unlike using clorox as we did). one of our postdocs made us move all our equipment to a hood room because she was too afraid to work. Even post-run gels scared her, its funny, my thesis lab would light up with a transilluminator. Imagine the days when we did southern blots and RFLP analysis. EtBr everywhere, you boiled the agarose with EtBr, p32 everywhere. And that wasn't the real dangerous stuff.

Don't feel too bad i used to use flour powdered latex gloves with dicyclohexylcarbodiimede, which may explain why I am sensitive to wheat now as well as allergic to latex. Nitrile is the way to go.

And in the lab where I work with P32 and S35, some people use C14... which lasts forever (from the practical viewpoint of the human lifespan), and they use it in pyruvate uptake assays, where it can ultimately be converted to CO2... sure they have something that is supposed to absorb the CO2 released...

A while back one of the CO2 lines to a cell incubator came off... if nobody had been in the room when it happened, the room could have filled with CO2, and the next one to come in could have shut the door behind them and passed out...

I'd rather just avoid the whole affair of working in a lab + the frustration of experiments that don't work.

Never used C14, had to deal with Cr51, which is considered a bad guy. Had my work space shut down because labmates S35 contamination, not his fault, he took the word of a collaborator that the sample had been desalted, ithadn't. P32, meh, us oldtimers used to sling that stuff around, it degrades quite rapidly. C14 is everywhere, you breath it all the time. The atmospheric nuke testing all but doubled the level. 125I, like crazy, doesn't scare me a bit.

CO2 can be absorbed by an alkaline scrubber industrial lime picks it up quite readily. we used to scrub hydrogen floride with limestone chips, course that releases CO2. If you have a good fiberglass filter you can water embed diatomaceous earth in a thin layer, degass distilled water or boil it and before it cools emulsify CaOH or CaO and trap it on the filter. Then remove the filter fiberglass down and lime layer up. As long as the humidity is over 80% you should be able to trap carbonic acid. You can even add a layer of powdered activated carbon on top to suck out the other isotopic organics. You just have to have a good high pressure fan unit to deal with the back pressure. You can buy bags of CaOH at any nursery.