Science Daily - HGT rapid between bacteria

[Psycho]

The fact a microbe lives within a human does not make it part of the human nor it does make human DNA 90% microbial - I think Psycho's analogies are trying to convey this point.

Actually my point is under a biochemical definition anything that passes through your gastrointestinal tract never enters your body at all, there is a tube from your mouth to your anus that forms a hole right through the middle of you which is segregated by sphincters, hence most matter leaving via the anus is classed as being egested rather than excreted or secreted as it isn't a product of metabolism.

 

Note that I using the medical definition of egested, excreted and secreted rather than the laymans.

Edited November 7, 2011 by Psycho

[CharonY]

I would call it a physiological, anatomical or (more generally)a biological definition rather than a biochemical one, but it is, of course correct. However, even if bacteria penetrate cells, quite often they are not really inside the cell either. They are still separated from the host's cytoplasm as they are still surrounded by the host's membrane (e.g. after endocytosis).

[kitkat]

The fact a microbe lives within a human does not make it part of the human nor it does make human DNA 90% microbial - I think Psycho's analogies are trying to convey this point.

 

 

 

Hmm the source you seem to be citing - the Human Microbiome project, is a major NIH funded investigation into human endosymbionts.... which would rather strongly suggest that scientists are not ignoring them - see publication list below. A major component of their research is investigating the role of the human microbiome in human health.

http://commonfund.nih.gov/hmp/sciencepub.aspx http://commonfund.nih.gov/hmp/initiatives.aspx#relationship

 

The fact we have endosymbionts just simply doesn't pose any challenges to the theory of evolution or current best practice species concepts, which it seems to be what you started out arguing.

 

 

 

 

 

No it's not, it's an organelle.

http://en.wikipedia.org/wiki/Mitochondrion

http://en.wikipedia.org/wiki/Organelle

 

Call it whatever you want but it still originates from endosymbiont bacteria

 

I am not trying disapprove the theory of evolution but I do question your interpretation of the facts.

[Arete]

Call it whatever you want but it still originates from endosymbiont bacteria

 

I am not trying disapprove the theory of evolution but I do question your interpretation of the facts.

 

Your interpretation of the facts appears to directly contradict observation on a number of fronts in this thread.

 

1) There is no documentation of widespread bacterial-human HGT in the article you alluded to.

2) There's no such thing as "The genome project" (It's the Human genome project, the 10k Genome project, the Honey Bee genome project....etc) and the Human microbiome project - which you were actually referring to - never stated that 90% of human DNA was microbial.

3) They actually stated that 90% of the cellular diversity of human body was bacterial. That's a very very different statistic in biological terms. By weight only about 10% of a human is symbionts. http://www.stephenja...d_bacteria.html

4) A considerable amount of scientific research is conducted into human symbiotic organisms, not none as you suggested. Spend 10 mins on google scholar and you'll get a feel for the quantity of literature on the subject.

5) Endosymbionts cannot be interpreted as being the same species as their host under any biological concept.

6) Mitochondria are hypothesized to have prokaryotic origins, but cannot be interpreted as actually being microbes under any biological concept, any more than my desk can still be considered to be a tree.

 

It's not that you're interpreting observations or facts differently, it's that the observations you're making are actually incorrect.

Edited November 8, 2011 by Arete

[kitkat]

Your interpretation of the facts appears to directly contradict observation on a number of fronts in this thread.

 

1) There is no documentation of widespread bacterial-human HGT in the article you alluded to.

2) There's no such thing as "The genome project" (It's the Human genome project, the 10k Genome project, the Honey Bee genome project....etc) and the Human microbiome project - which you were actually referring to - never stated that 90% of human DNA was microbial.

3) They actually stated that 90% of the cellular diversity of human body was bacterial. That's a very very different statistic in biological terms. By weight only about 10% of a human is symbionts. http://www.stephenja...d_bacteria.html

4) A considerable amount of scientific research is conducted into human symbiotic organisms, not none as you suggested. Spend 10 mins on google scholar and you'll get a feel for the quantity of literature on the subject.

5) Endosymbionts cannot be interpreted as being the same species as their host under any biological concept.

6) Mitochondria are hypothesized to have prokaryotic origins, but cannot be interpreted as actually being microbes under any biological concept, any more than my desk can still be considered to be a tree.

 

It's not that you're interpreting observations or facts differently, it's that the observations you're making are actually incorrect.

 

The article written by Stephen Gould explains it very well and this is why I formed my opinion that bacteria have a far greater influence then what is currently believed in these science forums.

 

The article written by Stephen Gould explains it very well and this is why I formed my opinion that bacteria have a far greater influence then what is currently believed in these science forums.

 

The widespread of HGT in bacteria was in the Science Daily article

[Psycho]

I would call it a physiological, anatomical or (more generally)a biological definition rather than a biochemical one, but it is, of course correct. However, even if bacteria penetrate cells, quite often they are not really inside the cell either. They are still separated from the host's cytoplasm as they are still surrounded by the host's membrane (e.g. after endocytosis).

I am sure that there are some intracellular symbiotic bacteria that live in the gut, but I can't think of any off hand, most forms intracellular bacteria in humans are just classed as pathogens due to the idea that they normally do damage to the host cell, I would be intrigued by any examples that could be found though.

 

 

Call it whatever you want but it still originates from endosymbiont bacteria

That is completely and utter irrelevant to anything at all, that happened way before humans and even mammals existed...

 

I am not trying disapprove the theory of evolution but I do question your interpretation of the facts.

You mean the meaning of the facts, rather than the interpretation, I understand this whole concept very well and its molecular basis and read about the topic frequently.

 

The article written by Stephen Gould explains it very well and this is why I formed my opinion that bacteria have a far greater influence then what is currently believed in these science forums.

 

No one has ever said they don't, you should probably actually read what has been written rather than just apparently making it up.

[kitkat]

I am sure that there are some intracellular symbiotic bacteria that live in the gut, but I can't think of any off hand, most forms intracellular bacteria in humans are just classed as pathogens due to the idea that they normally do damage to the host cell, I would be intrigued by any examples that could be found though.

 

 

 

That is completely and utter irrelevant to anything at all, that happened way before humans and even mammals existed...

 

 

You mean the meaning of the facts, rather than the interpretation, I understand this whole concept very well and its molecular basis and read about the topic frequently.

 

 

 

No one has ever said they don't, you should probably actually read what has been written rather than just apparently making it up.

 

The processes and interactions underlying symbiotic intracellular associations are still poorly understood by science so the facts aren't in yet.

[Psycho]

The processes and interactions underlying symbiotic intracellular associations are still poorly understood by science so the facts aren't in yet.

Well done, another completely irrelevant statement that doesn't support or disprove any of the statements made.

[kitkat]

Well done, another completely irrelevant statement that doesn't support or disprove any of the statements made.

 

Are you a microbiologist?

 

May I suggest reading dnaresearch.oxfordjournals.org/content/16/1/1.full which I might add views humans as a super organism. The microbial biota by far is the most biochemically active "organ" in the human body and they profoundly influence the physiology of its host. It is also believed that the microbial biota has co-evolved with the human host and its ancestors even before we looked human that goes all the way back to our origin.

[Arete]

Ok so for clarity -

 

1) You first made a preposition that an article posing widespread HGT between endosymbiotic bacteria and their human/animal hosts posed challenges for evolutionary theory. The forum demonstrated that even if this did occur, it didn't challenge current species concepts or evolutionary theory, the article was not actually proposing this at all.

 

The article was actually citing high rates of HGT in endosymbotic bacteria within vertebrate hosts - this is a long known phenomenon, the results of the initial Nature publication not unexpected, posing no challenges to current species concepts or evolutionary theory.

 

2) It seems like you're now postulating that considering bacterial endosymbionts and their hosts to be separate entities in terms of taxonomic classification/evolutionary history somehow trivializes or ignores their co-dependence?

 

Because this is simply wrong - the classification of evolutionarily distinct organisms as different is fundamental to further study characterizing co-evolution and co-dependence of organisms.

 

I mean, every heterotrophic organism on earth is dependent on autotrophs for survival. If we called every co-dependent group of organisms the same thing it would severely hinder any study of the actual systems themselves and wouldn't make any logical sense under current species concepts.

[Psycho]

Are you a microbiologist?

 

May I suggest reading dnaresearch.oxfordjournals.org/content/16/1/1.full which I might add views humans as a super organism. The microbial biota by far is the most biochemically active "organ" in the human body and they profoundly influence the physiology of its host. It is also believed that the microbial biota has co-evolved with the human host and its ancestors even before we looked human that goes all the way back to our origin.

Not really a hard premise to make that it is the most biochemically active, it is full other trillions of cells doing very similar things, it would be vastly inefficient for any of our organs to work in this fashion with limited cooperation. Furthermore biochemically active doesn't really mean anything, it makes no assertion of the complexity or nature of the activity, the more inefficient a process the more it has to occur to create the same product, that makes it worse not better.

 

As for referring to us as 'super organism' (in inverted commas as it is in the paper), it is a whimsical remark to be picked up by journalists hence the commas, as well as being utterly meaningless as it has no definition in laymans terms or scientifically.

 

Of course the microbiota has co-evolved with humans this hasn't ever been questioned, no one has ever claimed there aren't commensal bacteria.

 

I fail to see how that article helps your argument, all it does is prove your assertions wrong, while my affirmations that I have presented are based on scientific papers similar to that as well as practical experience and knowledge. What you have done is read it and not understand its content and then tried to present your intangible premises as truths.

Edited November 8, 2011 by Psycho

[kitkat]

Not really a hard premise to make that it is the most biochemically active, it is full other trillions of cells doing very similar things, it would be vastly inefficient for any of our organs to work in this fashion with limited cooperation. Furthermore biochemically active doesn't really mean anything, it makes no assertion of the complexity or nature of the activity, the more inefficient a process the more it has to occur to create the same product, that makes it worse not better.

 

As for referring to us as 'super organism' (in inverted commas as it is in the paper), it is a whimsical remark to be picked up by journalists hence the commas, as well as being utterly meaningless as it has no definition in laymans terms or scientifically.

 

Of course the microbiota has co-evolved with humans this hasn't ever been questioned, no one has ever claimed there aren't commensal bacteria.

 

I fail to see how that article helps your argument, all it does is prove your assertions wrong, while my affirmations that I have presented are based on scientific papers similar to that as well as practical experience and knowledge. What you have done is read it and not understand its content and then tried to present your intangible premises as truths.

 

You state we can process nutrients just fine without bacteria so why are they in us? I also thought that mitochondria evolved to take in oxygen produced by photosynthesis, is this wrong?

 

I just read that mitochondria consumes over 80% of the air we breathe and make over 90% of the energy our cells need to function. Air and food are metabolized by mitochondria. Our cell, eukaryotes likely evolved from two prokaryotes. Just because we can physically breathe oxygen, it is still converted by mitochondria. Mitochondria is currently called an organelle but its origin is believed to be a prokarote. This is strange since prokaryotes are not known to have organelles.

Edited November 9, 2011 by kitkat

[Psycho]

You state we can process nutrients just fine without bacteria so why are they in us?

They aren't in us, as I have already explained.

 

I also thought that mitochondria evolved to take in oxygen produced by photosynthesis, is this wrong?

This is correct, though how it was made isn't relevant, before you start going on about that for no reason.

 

I just read that mitochondria consumes over 80% of the air we breathe and make over 90% of the energy our cells need to function. Air and food are metabolized by mitochondria. Our cell, eukaryotes likely evolved from two prokaryotes. Just because we can physically breathe oxygen, it is still converted by mitochondria. Mitochondria is currently called an organelle but its origin is believed to be a prokarote. This is strange since prokaryotes are not known to have organelles.

The mitochondria will always be called an organelle, its DNA has been sequenced it has nothing left to hide. Mitochondria don't consume any air they utilize it for the greater good of the cell by creating a proton motive force, working to create ATP for the cell using distribution of labour.

 

No food is metabolised by the mitochondria.

 

How is it strange that the origin of the mitochondria are believed to be from endocytosis of a prokaryotic bacterium and prokaryotes don't have organelles, these two ideas are in no way related or relevant to any argument made or each other.

 

Stop making things up. I am now requiring a source for any of your information or I am no longer responding to it and you can continue to live in ignorance.

[kitkat]

They aren't in us, as I have already explained.

 

This is correct, though how it was made isn't relevant, before you start going on about that for no reason.

 

The mitochondria will always be called an organelle, its DNA has been sequenced it has nothing left to hide. Mitochondria don't consume any air they utilize it for the greater good of the cell by creating a proton motive force, working to create ATP for the cell using distribution of labour.

 

No food is metabolised by the mitochondria.

 

How is it strange that the origin of the mitochondria are believed to be from endocytosis of a prokaryotic bacterium and prokaryotes don't have organelles, these two ideas are in no way related or relevant to any argument made or each other.

 

Stop making things up. I am now requiring a source for any of your information or I am no longer responding to it and you can continue to live in ignorance.

 

The website is called The Mitochondrial and Metabolic Disease Center and this is where one of my sources explains what I said above.

 

The website is called The Mitochondrial and Metabolic Disease Center and this is where one of my sources explains what I said above.

 

My digestive system is inside my body, maybe yours isn't but everybody else does.

[Psycho]

The website is called The Mitochondrial and Metabolic Disease Center and this is where one of my sources explains what I said above.

 

That isn't what it say, I haven't specifically found it as you haven't linked to it, however it doesn't say what you have asserted it to.

 

Read all of this then you might actually understand mitochondria to a level so we can have an informed discussion about them and how they came about, bare in mind that the Mitochondrion may once been a bacteria but they no longer are and don't resemble one biochemically, they are an organelle and function as such.

 

My digestive system is inside my body, maybe yours isn't but everybody else does.

 

Then read through post #26 where I have already explained this already, then read post #27 to have CharonY agree with post #26.

Edited November 10, 2011 by Psycho

[kitkat]

That isn't what it say, I haven't specifically found it as you haven't linked to it, however it doesn't say what you have asserted it to.

 

Read all of this then you might actually understand mitochondria to a level so we can have an informed discussion about them and how they came about, bare in mind that the Mitochondrion may once been a bacteria but they no longer are and don't resemble one biochemically, they are an organelle and function as such.

 

 

 

Then read through post #26 where I have already explained this already, then read post #27 to have CharonY agree with post #26.

 

 

There is another website called Overview of Krebs-Reactions Electron Transport and Oxidative...

 

It explains the need for oxygen as an electron acceptor is the sole reason that we breathe air

 

jeb.biologists.org/content/210/12/i.2 The oxygen uptake in mitochondria is another website. Do you want more?

 

I think the problem we are having in communication is how we have a different viewpoint of microbes. Is your opinion of microbes is that they are biochemical conversion machines or something similiar to that?

Edited November 10, 2011 by kitkat

[Psycho]

There is another website called Overview of Krebs-Reactions Electron Transport and Oxidative...

 

It explains the need for oxygen as an electron acceptor is the sole reason that we breathe air

 

jeb.biologists.org/content/210/12/i.2 The oxygen uptake in mitochondria is another website. Do you want more?

 

I haven't specifically found it as you haven't linked to it, I am not going to try and look up every source you present if you won't link to it yourself (it also make it vastly easier/quicker for future/present readers to understand the subject), as half the time you just end up reading the wrong thing, it isn't hard to make a link, I even linked to a tutorial on it.

 

I think the problem we are having in communication is how we have a different viewpoint of microbes. Is your opinion of microbes is that they are biochemical conversion machines or something similiar to that?

 

Microbes are microbes and can't easily be defined as they are to diverse, organelles are a "biochemical conversion machine" in one light. You seem to be trying to make the premise that they are the same thing, I have already seen that coming and have been trying to stop you writing a whole post about it for my last 3.

 

I understand mitochondria very well, posting an article and not explaining the points you have taken from it (which maybe write or wrong, mitochondria aren't exactly the simplest things) isn't really helping the discussion, my aim was to get you to write your assertions with a link to the source you used so if incorrect for any reason (such as taking the information, using the premise that the mitochondria is a microbe) I could explain using your own source or if correct agree with them and add further information from a different source.

 

It explains the need for oxygen as an electron acceptor is the sole reason that we breathe air

 

Yes, but all they do is covert the chemical energy from O2 to a proton concentration gradient, how they get the O2 doesn't really matter for the life of a cell and therefore its intracellular mitochondria.

[kitkat]

I haven't specifically found it as you haven't linked to it, I am not going to try and look up every source you present if you won't link to it yourself (it also make it vastly easier/quicker for future/present readers to understand the subject), as half the time you just end up reading the wrong thing, it isn't hard to make a link, I even linked to a tutorial on it.

 

 

 

Microbes are microbes and can't easily be defined as they are to diverse, organelles are a "biochemical conversion machine" in one light. You seem to be trying to make the premise that they are the same thing, I have already seen that coming and have been trying to stop you writing a whole post about it for my last 3.

 

I understand mitochondria very well, posting an article and not explaining the points you have taken from it (which maybe write or wrong, mitochondria aren't exactly the simplest things) isn't really helping the discussion, my aim was to get you to write your assertions with a link to the source you used so if incorrect for any reason (such as taking the information, using the premise that the mitochondria is a microbe) I could explain using your own source or if correct agree with them and add further information from a different source.

 

 

 

Yes, but all they do is covert the chemical energy from O2 to a proton concentration gradient, how they get the O2 doesn't really matter for the life of a cell and therefore its intracellular mitochondria.

 

So we can communicate properly - prokaryotes, microbes, bacteria are all one and the same subject correct?

[kitkat]

Further research reveals that Mitochondria and Chloroplasts are referred to as organelles. These organelles reproduce like bacteria, replicate their own DNA and direct their own division.

[Arete]

Mitochondrial and chloroplast DNA is maternally inherited. They do not have independent evolutionary histories and are again, not equatable to bacteria under any existing system of biologically relevant terms.

[CharonY]

So we can communicate properly - prokaryotes, microbes, bacteria are all one and the same subject correct?

 

Nope. Backteria are prokaryotes but not all prokaryotes are microbes. All prokaryotes are microbes (which is not a taxonomic unit, though) but not all microbes are prokaryotes (mostly fungi are and sometimes other small, usually single-celled organisms are called microbes (as mentioned, they are not a real taxonomic unit, but rather a unspecific phrase).

 

An improtant point regarding organelles is that their evolutionary history (and future) since the merger is directly tied to the organism in question. This is not the case for the other bacteria colonizing their hosts.

[kitkat]

Nope. Backteria are prokaryotes but not all prokaryotes are microbes. All prokaryotes are microbes (which is not a taxonomic unit, though) but not all microbes are prokaryotes (mostly fungi are and sometimes other small, usually single-celled organisms are called microbes (as mentioned, they are not a real taxonomic unit, but rather a unspecific phrase).

 

An improtant point regarding organelles is that their evolutionary history (and future) since the merger is directly tied to the organism in question. This is not the case for the other bacteria colonizing their hosts.

 

The bacteria that live inside the host is its microbial biota - correct? Are they still prokaryotes?

[CharonY]

You mean like parasitic bacteria? Yes. But in contrast to mitochondria their evolutionary fate is not coupled. They can (and usually will) spread from host to host. Mitochondria do not have a free-living state anymore.

Edited November 30, 2011 by CharonY

[kitkat]

You mean like parasitic bacteria? Yes. But in contrast to mitochondria their evolutionary fate is not coupled. They can (and usually will) spread from host to host. Mitochondria do not have a free-living state anymore.

 

 

Do you view your own microbial biota as a parasitic relationship?