A rather dumb question about evolution, but still worth asking

Master Jedi Dan
Master Jedi Dan's picture
Posts: 289
Joined: 2007-05-30
User is offlineOffline
A rather dumb question about evolution, but still worth asking

Ok, so for all my life I've been taught ID.  This will be a rather dumb question about evolution, but how did plant life form?  I know that we have already shown that animal life formed from a single-celled organism (or something to that effect, pardon my limited education so far), but did plant life form from this same type of organism or did it come from something else?

Atheism is a non-prophet organization.


phooney
phooney's picture
Posts: 385
Joined: 2007-02-07
User is offlineOffline
Go the chloroplasts!

Go the chloroplasts!


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Plants and animal cells are

Plants and animal cells are actually extremely similar. They belong to one of three domains of different cell families. The first domain is Eubacteria. These are the common bacteria found everywhere on the planet. They are by far the most permeating life form in existence, and make up 90% of the dry biomass of the Earth. The second is the less common, more elusive Archaeabacteria, which tend to hide in the lithosphere surviving on an anaerobic cocktail of nutrients, but can also be found in bogs and lakes, and even our own stomachs.

The third and most familiar is the Eukaryota. These are what make up plant and animal cells. They are large and complex, almost 1000 times the size of the average bacteria. Each Eukaryotic cell is like a small city with lots of organelles swimming in a giant cytoplasm. Don't believe me? Check out that video on youtube called the inner life of the cell.

Eukaryotic cells can be classed as either plants or animals or fungi. Ancient Eukaryota originated as predators. They had a fluid highly flexible cell membrane that allowed them to envelope and capture nutrients. This function is retained in some cells like T-Cell lymphocytes, Leukocytes, and other cells in the immune system. This fluidity also allowed them to capture small bacteria. This is believed to be how our organelles in the cells came to be. There is a huge amount of compelling evidence that mitochondria, lyosomes, peroxisomes etc all the organelles inside the cells, are ancient bacteria that have since evolved into a symbiosis with the Eukaryotes.

So the ancient Eukaroytes were predators, trundling around and engulfing food. To look at how plant cells diverged from this, we need to understand a tiny little bacteria family called cyanobacteria.

These little bacteria may have been the first life forms in existence. They are known to have existed for almost 3.8 billion years. They perform a process called photohydrolysis. Sound familiar? It is a precursor to photosynthesis. These little organisms were the first photosynthetic organisms. Indeed, they were responsible for creating todays oxygen-based atmosphere. 

recall that the Primordial Eukaryotes would simply trundle along engulfing hapless prey? The plants were ancient Eukaryotes that swallowed the cyanobacteria. They became incorporated into the Eukaryotic machinery, allowing it to do what the bacteria does. Which is to obtain glucose by photohydrolysis.

And if the cells can do that...there is no need to chase after prey anymore. The plant cells were revolutionaries. They made the transition from hunting to farming around two billion years ago. So they lost their fluid bilayer (dont need it anymore) replacing it with a rigid cellulose wall which was useful for stacking chloroplast cells. They lost their ability to engulf. A process which by the way is called (this is my word of the day) phagocytosis.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


Master Jedi Dan
Master Jedi Dan's picture
Posts: 289
Joined: 2007-05-30
User is offlineOffline
Deludedgod, you never fail

Deludedgod, you never fail to amaze me.  Thanks for the answer! Smiling


Yellow_Number_Five
atheistRRS Core MemberScientist
Yellow_Number_Five's picture
Posts: 1390
Joined: 2006-02-12
User is offlineOffline
While deluded consitently

While deluded consitently rocks the house, I wanted to elabororate just a bit.

Animals actually predate TRUE plants. All TRUE plants (not monocellular protists and what not) postdate the Cambrian era, in which we saw a rapid evolution of animal species. There are several animal classes which predate the Cambrian, and before that we were dealing mainly we single cellular organisms.

Both plants and animals are believed to have been evolved from single celled life, so for example, if you consider a prokariotic bateria enveloping a chloroplast like structure and forming a symbiotic relationship a plant/animal hybrid, then yes. If not, then not really.

I gave a brief run down of cellular evloution in another thread:

It is theorized that cells developed from the incorporation of organelles into lipid capsules. Lipids form spherical capsules when placed in water due to them having an end which is hydrophobic (repels water) and and end which is hydrophillic (has an affinity for water). So for example, a lipid sphere could encapsulate a self-replicating molecule and something like this was probably the earliest thing we could call a cell. This replicator would now be protected from its environment to a degree, giving it a selective advantage. Other structures could then be incorporated that would provide mutual benefits to one another within this protected sphere. Again, giving an additional selective advantage. 

As deluded got into, there are two types of cells, prokaryotes which lack nuclei, and eukaryotes which have nuclei. Prokaryotes are the more primitive of the two and it is believed that eukaryotes evolved from them. The first eukaryote was likely a colony of prokaryotes that became incorporated.

Organelles, like mitochondria and chloroplasts, are the internal components of the cells, they are similar in function to your body's organs - they carry out chemical and catalyic reactions.

As an example, the mitochondria and chloroplasts of modern eukaryotes have featured similar to whole prokariotic cells. They contain their own DNA, which is circular, wheras nuclear DNA is linear. They also contain ribosomes for example. If these structures were incorporated into another cell, it would allow the new cell to perform aerobic respiration on its own - greatly increasing its efficiency and giving it a strong selective advantage. It would be a mutually beneficial arrangement - the "host" giving the mitochondria or chloroplasts organic material and the mitochondria or chloroplasts converting it into energy in the form of ATP. Eventually the resulting structure evolved to the point where the individual structures could not function properly without one another.


Check out::

Martin, W. and M. J. Russell. 2003. On the origins of cells: A hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions, Biological Sciences 358: 59-85. (technical)

 And a good linky: "Serial Endosymbiosis" http://www.geocities.com/jjmohn/endosymbiosis.htm



 

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

Atheist Books, purchases on Amazon support the Rational Response Squad server.


LeftofLarry
RRS local affiliateScientist
LeftofLarry's picture
Posts: 1199
Joined: 2006-02-12
User is offlineOffline
And a very related

And a very related topic. 

For those interested, here is a bit of new research presented just this month in the Journal Trends in Plant Science.  Fungi and animal cells have always been thought to be closer phylogenetically than animal and plants.  However, new research here presents that animal and plant eukaryotic cells (see explanation above of both deludedgod and yellow no. 5) share more commonalites than do fungi and animal cells.  

 For example, cancer occurs in both animal and plant cells, the underlying mechanisms are the same.  Another example is the enzymes that put RNA to work in a cell are similar in plants and animals, but not present in fungi or other organisms.

Plants have an immune system, much like animals and Stiller argues that certain proteins and genes, which are not present in other fungi, help plants and animals defend themselves against invading viruses and bacteria.

    Finally, some of the proteins used for nervous system signalling in animals are also found in plant neurobiology.  This is indeed interesting, plants actually have machinery that allows them to signal electrically, much like animal nervous systems.

 I think the underlying issue here is that evolution, acts on machinery as much as it acts on genes.  As Sean Carroll said, and I paraphrase, It's like teaching an old gene new tricks.

 

 

 

 

Atheist Books, purchases on Amazon support the Rational Response Squad server which houses Celebrity Atheists.


mileyp
Posts: 24
Joined: 2007-08-23
User is offlineOffline
I believe that the

I believe that the phagocytosis hypothesis is no longer thought to be the case with mitochondria. I think it is still  applies for plastids though.

William Martin and Miklos Muller proposed the hydrogen hypothesis in 1998 for the incorporation of the mitochondrion.

The hypothesis (as far as I understand it) claims that methanogens in the deep sea and marshes formed symbiotic relationships with external anaerobic eubacteria (hydrogenosomes) which released hydrogen and carbon dioxide as waste products of the respiratory chain. The methanogens, like most bacteria would have had rigid cell walls preventing phagocytosis. Instead they would line up next to the eubacteria slowly growing around them. Later they engulfed them and incorporated them inside.

 The problem with the phagocytosis hypothesis is that phagocytosis requires a lot of energy because the cytoskeleton must be manipulated. It would seem reasonable to assume that mitochondria would be necessary before phagocytosis could evolve.

Also the phagocytosis hypothesis would predict that some primitive ancestors of eukaryotes (ie with a nucleus) would not have mitochondria. These organisms have not been found.

 I came across this hypothesis whilst reading "Power, Sex, Suicide: Mitochondria and the Meaning of Life" by Nick Lane. I haven't finished yet, but it seems an excellent book so far. It covers the hypotheses about the origin of life, as well as the origin of eukaryotes in more detail.


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
I am quite sure that

I am quite sure that Endosymbiant phagocytosis is still the leading theory to explain plastids and mitochondria.

Quote:

The methanogens, like most bacteria would have had rigid cell walls preventing phagocytosis.

That does not matter. What matters for the engulfing of smaller organisms by eukaryotic proto-cellular material is the fluidity of the choline-phosphate-glycerol bilayer. As long as the engulfing layer is fluid enough to undergo phagocytosis, then the rigidty of the cell wall of the bacteria should be able to be withstood. This explains why that after the proto-eukaryota that diverged from the original line captured cyanobacteria, thereby allowing photohydrolosis, their own cell walls became rigid cellulose so that they could structure plant-life, via the stacking of chloroplasts and paliside cells to form the spongy mesophyll and palaside layers.

However, methanogens are anoxic. They produce methane. While it has been speculated the lithotropes and chemotrophes such as methanogens may play an important role in some non-oxygen based exobiology where CH4 might be dominant, the problem for eubacteria trying to survive after the oxygen catastrophe would invariably be...oxygen, that which they created. They needed to be able to utilize oxygen (Kreb's cycle aka citric acid cycle) otherwise they would die. Using sulfer dioxide as an anoxic agent for pumping ions through a H+ pump to form ATP (electron transport chains) would not help them. In order to survive, they would need to have utilized, not sulfer dioxide, but oxidative phosphorylation.

The problem with this is that mitochondria actually predate hydrogenosomes, at least as far as I know. Methanogens are anoxic chemotrophs which use Adenosine triphosphate without molecular oxygen respiration (ie the Krebs cycle), and hydrogenosomes are, well, hydrogen-based anoxic organisms. If I recall, they do have a symbiant role in some Eukaryota as well as archaebacteria (fungi) but all Eukaryota have mitochondria, which predate hydrogenosomes.

To be sure, hydrogenosomes play an important role in symbiosis with methanogens but this is not an accepted explanation for the rise of the Eukaryota after the oxygen catastrophe. For that, we have the engulfing of cyanobacteria and mitochondria by lipid bilayers which form by ampipathism, creating proto-eukaryota. Whatever simple fluid cells existed without a nucleus have long since been outphased, much as RNA has been outphased as a method of vertical and horizontal transfer.

If we examine a hydrogenosome, it is a very stripped down version of a mitochondria which is found inside lithotrophic archaeabacteria. Now, the mitochondria in different Eukaryotic species have mtDNA genomes stripped down in varying degrees mostly because the bulk of mtDNA has migrated via plasmid encapsulation (xenologous transfer) into the intracellular compartment of the nucleus. But there is no hydrogenosome DNA found in any Eukaryota. We have only found them in lithotrophic symbionts.

Quote:

Also the phagocytosis hypothesis would predict that some primitive ancestors of eukaryotes (ie with a nucleus) would not have mitochondria. These organisms have not been found.

I never came across endosymbiosis as having predicted that there should still be any proto-eukaryota left. They were simply outphased, in much the same way that there are no RNA based organisms in existence anymore, as far as we know.

 

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


mileyp
Posts: 24
Joined: 2007-08-23
User is offlineOffline
Quote: That does not

Quote:
 That does not matter. What matters for the engulfing of smaller organisms by eukaryotic proto-cellular material is the fluidity of the choline-phosphate-glycerol bilayer

I meant that the methanogens wouldn't be able to phagocytose (unless that is what you meant?)

Quote:
The problem with this is that mitochondria actually predate hydrogenosomes, at least as far as I know. Methanogens are anoxic chemotrophs which use Adenosine triphosphate without molecular oxygen respiration (ie the Krebs cycle), and hydrogenosomes are, well, hydrogen-based anoxic organisms. If I recall, they do have a symbiant role in some Eukaryota as well as archaebacteria (fungi) but all Eukaryota have mitochondria, which predate hydrogenosomes.

Sorry, I meant that hydrogenosomes and mitochondria have a common ancestor, this suggests that the ancestor might have been able to perform both metabolic functions. The hydrogen hypothesis suggests that it was the hydrogen-producing function that was more advantageous to the original eukaryote.

Quote:
all Eukaryota have mitochondria, which predate hydrogenosomes

I believe several species of fungi have hydrogenosomes only, though I'm not sure, this also might be a later evolutionary step. Also there are several examples of eukaryotes without mitochondria at all, the so-called archezoa. [There is evidence that these cells used to have mitochondria and then lost them because they were superfluous.]

The evidence for methanogens being the earliest predecessor of the eukaryotic cell, cellular DNA relating to informational functions (such as DNA replication, cell membrane structure etc.) is most closely related to methanogens.

Also eukaryotic histones are closely related to those in methanogens.

With this evidence in mind, if the first eukaryotic cell arose from a mitochondrial precursor alpha-proteobacterium merging with a methanogen, phagocytosis would not be possible. This is because methanogens have rigid cell walls (not peptido-glycan like bacteria but still rigid).

Quote:
I never came across endosymbiosis as having predicted that there should still be any proto-eukaryota left

Does endosymbiotic phagocytosis suggest mitochondria were engulfed after eukaryotes had become eukaryotes (as in had a nucleus)?

Because if it does, and I believe it does, but I'm slightly hazy on that detail, it would suggest that at some point there would be a* eukaryotic cell without some form of mitochondrial ancestor. This would not necessarily be alive today, because as you say it would quickly be phased out and out-competed so I suppose my point was a little pointless!

*p.s. do you think that should read "an eukaryotic"? Because "an" sounds strange in the context! :-S

p.p.s. I going to sleep now, so if you reply, I won't be able to reply until tomorrow (UK time so in around 10 hours)


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Quote: I meant that the

Quote:

I meant that the methanogens wouldn't be able to phagocytose (unless that is what you meant?)

But methanogens are prokaryota. Prokaryota have rigid cell walls. They cannot phagocytose anyway. Only Eukaryota can do this.

Quote:

Sorry, I meant that hydrogenosomes and mitochondria have a common ancestor, this suggests that the ancestor might have been able to perform both metabolic functions.

They probably do, but we have found no evidence of such a bacteria. Although given how many species were eliminated during the Oxygen catastrophe, and how many more remain unclassified, this is hardly suprising. Still, there is no reason to suppose that such an organism was indeed the original prokaryote when the evidence from xenlogous transfer of the mitochondrial genome via plasmid encapsulation indicates that they were the original organisms which we phagocytosed by the proto-Eukaryota. It is very difficult to now the precise chain of events that occurred 2 billion years ago, but this is the most workable theory we have. It is indeed possible that the mitochondria were outphasing some sort of proto-bacteria from which it descends which originally was phagocytosed by proto-eukaryota, but without further evidence, conjecuture is pointless.

Quote:

The hydrogen hypothesis suggests that it was the hydrogen-producing function that was more advantageous to the original eukaryote.

Unless some original Eukaryotic species actually mananged to survive lithotrophically, which I doubt (conditions too violent), there would be no advantage to hydrogen metabolization, Eukaryota only arose as a result of the Oxygen Catastrophe, so only mitochondrial phagocytosis would have a selective benefit.

Quote:

I believe several species of fungi have hydrogenosomes only,

Do they? I have never heard that, but then, I am not a mycologist. Care to cite any? I will say that fungi are remarkably metabolically heterotrophic, so you might be right.

Quote:

though I'm not sure, this also might be a later evolutionary step.

We would notice it in the genome of any fungi with hydrogenosomes, as some of the DNA would have migrated to the nucleus.

Quote:

Also there are several examples of eukaryotes without mitochondria at all, the so-called archezoa.

Archezoa as a hypothesis was abandoned by the  molecular evolutionary biology community a while ago. The problem is that molecular phylogeny does not support any account of any Eukaryota having had a pre-mitochondrial bacterial symbiont, as we would be able to incorporate that into the phylogeny tree via its descendants or those who outphased it even if was no longer around, because symbionts leave very distinct signs on the host genome. We would recognize it. In this case, with archezoa, molecular biologists were unable to place it on any phylogeny, so we ditched it.

Quote:

The evidence for methanogens being the earliest predecessor of the eukaryotic cell, cellular DNA relating to informational functions (such as DNA replication, cell membrane structure etc.) is most closely related to methanogens.

Methanogens being the prdecessors of Eukaryotic cells? I doubt it. I think you mean the predecessor of a symbiotic organism of Eukaryotic cells. As an archaeabacteria, it has a rigid cell wall and the DNA replication processes are plasmid-based template polymerization, just like any other bacterial organism whose DNA is encapsulated in a circular ring without an intracellular compartment. This makes it totally different to Eukaryota, which are (or were, the plants diverged later) fluid membranes which evolved cykoskeletal structures and ampipathic bilayer (an autocatalytic function of any basic cell membrane inside a dipolar medium like water). Most molecular biologists believe that Eukaryota are or were originally plasma membranes which would encapsulate bacterial organisms, although obviously the genome (even ESPs) is directly descendent from bacteria, however, to my knowledge, there is no single archaea or eubacteria upon which this phylogeny is drawn. There is a schism in molecular evolutionary biology about this. Some believe that all three groups are directly descendant from a common ancestor, or if the three were originally unseperated gene groups which promiscuously exchanged genes before their separate ways. Regardless, due to the complexity of the genome and ESPs in particular, I am very sure that molecular biologists are not sure about any single bacteria which has the closest relationship to proto-Eukaryota (especially given how many bacteria exist without our knowledge! Say 99%)

Quote:

Also eukaryotic histones are closely related to those in methanogens.

This I definitely do not follow. Histones are Eukaroytic proteins, among the most highly conserved ESPs, for the construction of octameric nucleosomes for the packaging of DNA into the intracellular compartment of the nucleus. I know that a handful of archaea have histones as well, but from that we must not draw any hasty conclusions. For one, histones are among the most highly conserved proteins in the whole proteome, two, there are thousands of unclassified Eukaryota-specific proteins, and most molecular biologists would believe that the recombination of proteins from many different prokaryota made contributions to the primordial Eukaryotic genome, so the jury is still out on that one.

Quote:

With this evidence in mind, if the first eukaryotic cell arose from a mitochondrial precursor alpha-proteobacterium merging with a methanogen, phagocytosis would not be possible. This is because methanogens have rigid cell walls (not peptido-glycan like bacteria but still rigid).

But Eukaryotic cells do not arise from bacteria. The symbiotic organisms and the genome do arise from bacteria, but the actual cell was definitely originally an encapsulation of bacteria by choline-glycerol-phosphate bilayers. The dominant theory in molecular evolution is that mitochondria were a bacterial organism which was the original organism phagocytosed by proto-eukaryota for purposes of a reciprocal relationship due to the Oxygen catastrophe. Having a lithotropic organism form a symbiosis would have no evolutionary advantage (it wouldn’t work anyway since lithotropes live in the Earth’s crust). So a methanogen would have nothing to gain from the symbiosis, only a metabolizing organism which needed to be protected from oxygen.

Quote:

Does endosymbiotic phagocytosis suggest mitochondria were engulfed after eukaryotes had become eukaryotes (as in had a nucleus)?

We don’t have enough information to answer that question.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


mileyp
Posts: 24
Joined: 2007-08-23
User is offlineOffline
Quote:

Quote:

Do they? I have never heard that, but then, I am not a mycologist. Care to cite any? I will say that fungi are remarkably metabolically heterotrophic, so you might be right

Neocallimastigomycota is the only phylum I can find at the moment that have only hydrogenosomes.

Quote:
Archezoa as a hypothesis was abandoned by the molecular evolutionary biology community a while ago. The problem is that molecular phylogeny does not support any account of any Eukaryota having had a pre-mitochondrial bacterial symbiont, as we would be able to incorporate that into the phylogeny tree via its descendants or those who outphased it even if was no longer around, because symbionts leave very distinct signs on the host genome. We would recognize it. In this case, with archezoa, molecular biologists were unable to place it on any phylogeny, so we ditched it

I believe that eukaryotes without mitochondria today have all been shown to have mitochondrial genes remaining in their genomes, indicating that they once had mitochondria and then lost them. But that was why I said "the so-called archezoa"

Quote:
Methanogens being the prdecessors of Eukaryotic cells? I doubt it. I think you mean the predecessor of a symbiotic organism of Eukaryotic cells

sorry, that is what meant.

Quote:
As an archaeabacteria, it has a rigid cell wall and the DNA replication processes are plasmid-based template polymerization, just like any other bacterial organism whose DNA is encapsulated in a circular ring without an intracellular compartment. This makes it totally different to Eukaryota, which are (or were, the plants diverged later) fluid membranes which evolved cykoskeletal structures and ampipathic bilayer (an autocatalytic function of any basic cell membrane inside a dipolar medium like water).

I think that archaebacteria use eukaryote-like initiation and elongation factors during DNA translation. Also they use TATA Binding Proteins (TBP) during transcription which I believe are very similar to the equivalent eukaryotic proteins.

Quote:
which evolved cykoskeletal structures

I believe that the eukaryotic cytoskeleton is also thought to have prokaryotic origins, this hypothesis arose from observed genetic similarites between eukaryotic cytoskeleton proteins (esp. tubulin and actin).

Quote:
Mileyp wrote:
Also eukaryotic histones are closely related to those in methanogens
This I definitely do not follow. Histones are Eukaroytic proteins, among the most highly conserved ESPs, for the construction of octameric nucleosomes for the packaging of DNA into the intracellular compartment of the nucleus. I know that a handful of archaea have histones as well, but from that we must not draw any hasty conclusions. For one, histones are among the most highly conserved proteins in the whole proteome, two, there are thousands of unclassified Eukaryota-specific proteins, and most molecular biologists would believe that the recombination of proteins from many different prokaryota made contributions to the primordial Eukaryotic genome, so the jury is still out on that one.

What is an ESP, I am guessing an 'Evolutionary Stable Protein'?

see: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=147304&blobtype=pdf

Though if I understand what you wrote, eukaryotic precursors (are these called protoeukaryotes?) could have absorbed these genes via horizontal transfer? Though this is thought to be unlikely according to the authors (half-way down page 4).

I agree though that this is pretty ambiguous evidence for archaeal ancestry.

Quote:
But Eukaryotic cells do not arise from bacteria. The symbiotic organisms and the genome do arise from bacteria, but the actual cell was definitely originally an encapsulation of bacteria by choline-glycerol-phosphate bilayers.

I am assuming that a choline-glycerol-phosphate bilayer is the same as the current eukaryotic phospholipid bilayer (which is how I was taught it).

How would the proto-eukaryote generate energy? By glycolysis alone? Or by forming a chemo-osmotic potential across a membrane somewhere? (like bacteria do).

Does phagocytosis not require the cell to be large? This qualification would be disadvantageous to a mitochondria-less cell. A large cell would have a low volume to surface area ratio, causing diffusion (especially of glucose and other respiratory substrates) to take longer and therefore be less efficient. And therefore disadvantageous.

Wouldn't manipulation of the cytoskeleton to perform phagocytosis require a lot of energy? (I'm assuming that the cytoskeleton works in a similar way to muscle fibres).

For me the evidence seems to indicate that phagocytosis would require mitochondria to provide plentiful energy.

Quote:
The dominant theory in molecular evolution is that mitochondria were a bacterial organism which was the original organism phagocytosed by proto-eukaryota for purposes of a reciprocal relationship due to the Oxygen catastrophe. Having a lithotropic organism form a symbiosis would have no evolutionary advantage (it wouldn’t work anyway since lithotropes live in the Earth’s crust). So a methanogen would have nothing to gain from the symbiosis, only a metabolizing organism which needed to be protected from oxygen

Unfortunately I do not have the necessary information at the moment, there was a very neat explanation/rationalisation of this problem. I'll have to get back to you in a bit.


mileyp
Posts: 24
Joined: 2007-08-23
User is offlineOffline
for some reason my post

for some reason my post isn't displaying, anyone know what to do?


mileyp
Posts: 24
Joined: 2007-08-23
User is offlineOffline
by the way, here is a link

by the way, here is a link to Martin's and Muller's paper:

http://www.molevol.de/publications/59.pdf

if you can't see my other post, I think that if you click reply you should be able to see it

 


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Quote:

Quote:

Neocallimastigomycota is the only phylum I can find at the moment that have only hydrogenosomes.

Of course. Anaerobic protozoans. I forgot. Neocallimastogomycota are not the only one, btw. There are several families of anaerobic protozoans. That is the Excavata class of Eukaryotic protozoa, which lack mitochondria. That is why this small class of Eukaryota are called the amitochondrites.

However, I thought our debate was whether or not a primordial Eukaryotas original symbiont was some pre-mitochondrial organism which was outphased. There are three groups of Eukaryotic amitochondrial organisms, the microsporidians, archameboae, and metamondas. However, these are a not a separate phylogenic branch. There were no amitochondrial Eukaryotes directly after the Oxygen catastrophe. These organisms retain organelles which came after the mitochondrial protobacteria, there was no branch-off during the Catastrophe in which some Eukaryota did not engulf the mitochondrial bacteria. All Original Eukaryotes had mitochondrial bacteria, and these three groups lost it (we used to think it was the other way around, until genomic analysis confirmed this was a long branch error), which is why they have mtDNA inside the nuclear envelope.

I just realized we have been arguing about nothing. There is no such independant organism as the mitochondria, just as there is no such organism as the chloroplast. These are stripped down protobacteria which lost the bulk of their molecular functions as they were incorporated into the machinery of the eukaryotic intracellular vescicular traffic. Chloroplasts are, or were, cyanobacteria, outside the Eukaryota, no one calls them chloroplasts, because they are not.

So, all this time, when I have been using the phrase mitochondria I was referring not to the organelle, but the protobacteria which was engulfed that later became the mitochondria. So unless I am mistaken, I am arguing that some protobacteria was engulfed by Eukaryota which was stripped down into a Eukaryotic organelle which is the mitochondria, and that a few groups after the catastrophe lost it. You are arguing that the original Eukaryota had some sort of other endosymbiont which was outphased by the protobacteria which became mitochondria (such as hydrogenosomes), correct? This is the hydrogen hypothesis, which implies that Eukaryotic organelle machinery is chimera based from the shared relationship between an anaerobic eubacteria and a lithotrophic methanogen, correct? Which would indicate that modern Eukaryota have a cell machinery derived from the other two domains of life directly?

Quote:

I believe that eukaryotes without mitochondria today have all been shown to have mitochondrial genes remaining in their genomes, indicating that they once had mitochondria and then lost them. But that was why I said "the so-called archezoa"

Yes, but this is the opposite of our argument, unless I am mistaken. In no way am I denying that the anaerobic Eukaryota once had mitochondria in much the same way that I would not deny that plant cells used to have phospholipid bilayers.

Quote:

I think that archaebacteria use eukaryote-like initiation and elongation factors during DNA translation.

All cellular Elongation Factors have direct relations, even ESPs to the prokaryotic Ef-TU factor. Sorry, I should have explained what an ESP is. An ESP is a Eukaryotic Specific Protein. Any protein which is unique to Eukaryotes and is not possessed or needed by any prokaryotic cellular machinery is an ESP. ESPs are believed to have been built from recombinative innovation from the proteome of Prokaryota.

Quote:

Also they use TATA Binding Proteins (TBP) during transcription which I believe are very similar to the equivalent eukaryotic proteins

Yes, that is indeed true, fair enough

Quote:

I believe that the eukaryotic cytoskeleton is also thought to have prokaryotic origins, this hypothesis arose from observed genetic similarites between eukaryotic cytoskeleton proteins (esp. tubulin and actin).


Yes, all Eukaryotic fibrous ESPs have homologous and recombinative relationship to fibrous proteins in prokaryota, even if the ESPs have adapted for the purpose of cytoskeletal structure. For example, tubulin is definitely a protein which we can trace easily back to firbrous proteins before Eukaryota, but its function as the modular domain for the assembly of microtubules is mostly Eukaryota specific (however, the cytoskeletal mechanism can also be present in prokaryota) . This relationship is evident in any examined fibrous protein, such as keratin, elastin, collagen etc. Most molecular biologists have concluded that ESPs are constructed by module domain reassembly from the prokaryotic proteome.

Quote:

I am assuming that a choline-glycerol-phosphate bilayer is the same as the current eukaryotic phospholipid bilayer (which is how I was taught it).

Yes, you may use either term

Quote:

How would the proto-eukaryote generate energy? By glycolysis alone? Or by forming a chemo-osmotic potential across a membrane somewhere? (like bacteria do).

Put money on glycolysis and fermentation

 

Must go now. Will finish questions on cytoskeletal role in phagocytosis and cytoplasm later. Although, I can see the problem, that the Eukaryota originally would have started out as predators would requisite that they already have a cytoskeletal mechanism for movement and another intracellular compartment to keep the genome encapsulated and safe from the violent movement of the cell as it moved around to engulf bacteria. So they would have needed a source of energy before the evolution of oxidative phosphorylation metabolic pathways so that they could develop such a structure for their ability of preying upon the oxyphobic bacteria, and I think that the most ubiquitous pathway for this would definitely have been glyolysis and fermentation as a pathway before the engulfing of mitochondria. After all, cells can respirate anaerobically (like the lactic acid pathways), it is just much less efficient. Glycolysis still produces two NADH and two hydrolyzed ATP into ADP+ Pi for each glucose molecule, for which two surplus ATP are generated for the ones that were consumed. Obviously, however, this is nothing compared to the Krebs cycle and the oixdative phosphorylation that follows it, which produces three NADH, one FADH2, one GTP, and the electron transport caused by the reducing power of NADH produces thirty ATP for each turn of the cycle, so obviously the evolution of the Kreb's cycle and the use of a proton-powered electrochemical gradient for the phosphorylation of Adenosine Diphosphate would been tremendously advantegeous.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism


mileyp
Posts: 24
Joined: 2007-08-23
User is offlineOffline
from an earlier

from an earlier post: 

Quote:

Having a lithotropic organism form a symbiosis would have no evolutionary advantage (it wouldn’t work anyway since lithotropes live in the Earth’s crust). So a methanogen would have nothing to gain from the symbiosis, only a metabolizing organism which needed to be protected from oxygen.

Here is the rationalisation for the evolutionary steps. I hasten to add that the hypothesis is simply educated speculation, I don't say that this is the only way eukaryotic life could have arisen. The evidence does seem compelling though.

Hydrogenosomes and Mitochondria almost definately shared a common ancestor. The evidence for this is quite extensive.

see: http://mbe.oxfordjournals.org/cgi/content/full/17/1/202

Martin and Muller proposed that the ancestor could have had genes for both aerobic respiratory chains and for hydrogen-producing biochemistry. Though this is quite a jump, discovery of versatile bacteria supports the feasibility of this assumption. Rhodobacter can perform photosynthesis, lithotrophy, and aerobic and anaerobic respiration.

During the oxygen catastrophe, sulphur in the oceans would be oxidised into sulphate (S + 2O2 -> SO4[2-] via several steps). This would cause a rise in sulphate-reducing bacteria (SRB). These bacteria use hydrogen to reduce sulphate to sulphide. Sulphide is reduced further to hydrogen sulphide. An increase in SRB population in this time period is supported by geological evidence of H2S build up on the ocean floor. H2S is denser than water so would sink. This condition persisted for 1 billion years 2 billion years ago (around the time that eukaryotes are thought to have first formed) (ps I say formed rather than evolved because I am not sure if symbiosis counts as evolution, does it?)

Since SRBs use hydrogen to reduce sulphate, methanogens would be directly competing for hydrogen. If the proto-mitochondria was a versatile organism, then it would survive both in the anoxic environment of the methanogens and in the newly oxygenated environment. Methanogens would move close to these organisms because the hydogen produced would be hugely beneficial in the period of high competition. Over time the methanogenic cytoskeleton would evolve to cause the methangen to more closely 'fit' the proto-bacterium. Eventually the proto-bacterium would be engulfed completely. This raises a problem because the proto-bacterium would no longer be able to absorb food efficiently.

It was proposed that the proto-bacterium could have passed over the genes for food import and modification to the methanogenic host cell. This could have occured via horizontal transfer when the proto-bacterium dies. In the postulated millions of trials, the correct genes would feasibly be absorbed.

The competition with SRBs would now force the methanogens to oxygenated areas where nutrients would be abundant. The aerobic function of the symbiotic bacteria would now be incredibly useful. In later evolution perhaps the hydrogenosomic function would be lost forming mitochondrial precursors.

The problem with this hypothesis for me is that it seems unlikely that the proto-bacteria would retain both respiratory pathways. Bacteria lose unused functions extremely quickly as I'm sure you know.

Also it doesn't explain why eukaryotic cells have bacteria-like cell membranes rather than archaeal ones (achaea form ether bonds between glycerol and fatty acid chains rather than ester bonds, also they use a different stereoisomer of gycerol phosphate).

This hypothesis can also explain how the nuclear envelope might have arisen. If, by horizontal transfer, genes for building the proto-bacterial cell membrane were transferred into the proto-eukaryote genome, and then the targetting sequence on the phospholipids were deleted by mutation. These lipids would build up around the cell DNA, lipids form vesicles spontaneously, a primitive nuclear envelope and endoplasmic reticulum might have formed.

Quote:
However, I thought our debate was whether or not a primordial Eukaryotas original symbiont was some pre-mitochondrial organism which was outphased. There are three groups of Eukaryotic amitochondrial organisms, the microsporidians, archameboae, and metamondas. However, these are a not a separate phylogenic branch. There were no amitochondrial Eukaryotes directly after the Oxygen catastrophe. These organisms retain organelles which came after the mitochondrial protobacteria, there was no branch-off during the Catastrophe in which some Eukaryota did not engulf the mitochondrial bacteria. All Original Eukaryotes had mitochondrial bacteria, and these three groups lost it (we used to think it was the other way around, until genomic analysis confirmed this was a long branch error), which is why they have mtDNA inside the nuclear envelope

That was what I was trying to say! The amitochondria point was really just a passing digression. Also before the phylogeny of these organisms was ascertained, they were held up as proofs that Margulis' original endosymbiotic theory was true. So I suppose the point is slightly relevant.

Quote:
So, all this time, when I have been using the phrase mitochondria I was referring not to the organelle, but the protobacteria which was engulfed that later became the mitochondria.

That is what I assumed.

Quote:
 So unless I am mistaken, I am arguing that some protobacteria was engulfed by Eukaryota which was stripped down into a Eukaryotic organelle which is the mitochondria, and that a few groups after the catastrophe lost it. You are arguing that the original Eukaryota had some sort of other endosymbiont which was outphased by the protobacteria which became mitochondria (such as hydrogenosomes), correct? This is the hydrogen hypothesis, which implies that Eukaryotic organelle machinery is chimera based from the shared relationship between an anaerobic eubacteria and a lithotrophic methanogen, correct? Which would indicate that modern Eukaryota have a cell machinery derived from the other two domains of life directly?

yes ... I named the hydrogen hypothesis as my source in my first post. I believe that eukaryotes and archaea have many such similarities. Such as their ribosomes are both inhibited by diphtheria which doesn't inhibit bacterial ribosomes, also histones as I said above, discovered by John N Reeve at Ohio State University.


aiia
Superfan
aiia's picture
Posts: 1923
Joined: 2006-09-12
User is offlineOffline
mileyp wrote: for some

mileyp wrote:
for some reason my post isn't displaying, anyone know what to do?
FIXED

Most of us use the Mozilla Firefox browser which displayed your post correctly

People who think there is something they refer to as god don't ask enough questions.


lpetrich
lpetrich's picture
Posts: 148
Joined: 2007-05-14
User is offlineOffline
Any opinion of the

Any opinion of the Hartman-Fedorov hypothesis? The origin of the eukaryotic cell: A genomic investigation

It states that the ultimate eukaryotic host was outside of the two prokaryotic domains, being a cell that they call a "chronocyte". This organism had an RNA genome instead of a DNA one; it branched off of the ancestors of the prokaryotes before those ancestors invented DNA.

Its first endosymbiont was an archaeon, which explains that informational system being closer to Archaea than to Bacteria. This organism gradually accumulated its host cell's genome by way of reverse transcription, but much of the RNA processing remained, because its presence had become necessary for many of the genes to work right.

After that were various symbionts and gene contributions from Bacteria, including the ones that became the mitochondria and the chloroplasts.

 


deludedgod
Rational VIP!ScientistDeluded God
deludedgod's picture
Posts: 3221
Joined: 2007-01-28
User is offlineOffline
Very interesting. There are

Very interesting. There are still loads of unaccounted for ESPs and we need to be able to solve them, if they cannot be found to be homologously related to the Prokaryotic Empire of archaea and bacteria. It is well known that aechae bear greater resemblance to Eukaryota in terms of cellular machinery for replication, transcription, translation and repair of genetic information and that bacteria better resemble the eukaryotic methods of metabolism and energy conversion, anabolic and catabolic process. The usual hypothesis is that Eukaryotic genomes, at least the primordial ones, arose as a result of the recombination of archaea and bacteria. The problem, as the abstract pointed out, is ESP. However, we were not actually discussing the arisal of Eukaryotic genomes, instead the original symbiont of whatever was the class of cells after the oxygen catastrophe which took up what are now called mitochondria and chloropolasts. It seems to be a workable hypothesis for the ESP problem, However, I am very suspicious of the postulatation of an RNA-based organism, long since believed to have been outphased. We have never come across an RNA organism and there is no reason to suppose that we will. I am very suspicious towards the idea that the cell divergence we see today is the result of divergence that occured before the rise of DNA, in which case, we should see a clade of totally self-containted RNA based organisms. It would be fascinating, but I am a realist. RNA organisms disappeared before the arisal of cyanobacteria.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

-Me

Books about atheism