The 90% of microbial DNA in our DNA

[kitkat]

The Genome Project discovered that our DNA is 90% microbial and only 10% is ours. How did 90% get there if it is not done through HGT or LGT. Biologists state they do not see HGT in mutations by bacteria in our DNA.

 

Another question is does a newborn baby also have 90% microbial DNA and if so how are they determined sterile at birth?

 

We share 1% of our DNA with chimps. The remaining 9% is related to what other organisms?

[dttom]

If I remember right, we share merely 65% with bacteria, and this number does not need to bother with HGT nor LGT, consider all organism back converge to single origin, it is not diffcult to predict such a major similarity. And great morphological difference could be resulted not simply from informational blueprint but differential utilisation.

 

Yes, sterile infants also share the percentage, as a species.

 

We should share 99% with chimps... Not sure about what your question asking is ..about.

[CharonY]

More to the point, what is supposed to be "our" DNA. Gene sequences that are exclusively found in humans as compared to whom? Those are very little (if any). As we share common ancestries we share all the basic sequences with our relatives. The only genes that could be specific are those that arose after the last speciation event. But that was not that long ago and should account for a very little.

[kitkat]

Has science provided any explanation as to why our DNA is 10 to 1 in microbial DNA. What use does it serve? It gives you the impression that we are a species of colonized bacteria. If this is true why did they not just make all life look the same since they are viewed as mindless biochemical machines/germs etc. If are just mobile food processing machines that aid in preventing their enemies from invading our bodies, why bother giving us this illusion that we are unique?

[CharonY]

I merged the topics, as both posts essentially ask the same.

[cypress]

Has science provided any explanation as to why our DNA is 10 to 1 in microbial DNA. What use does it serve? It gives you the impression that we are a species of colonized bacteria. If this is true why did they not just make all life look the same since they are viewed as mindless biochemical machines/germs etc. If are just mobile food processing machines that aid in preventing their enemies from invading our bodies, why bother giving us this illusion that we are unique?

 

If you look at the research more closely what you will find is that by some percentage estimated between 10% and up to 90% of the expressed sequences that generate proteins share a degree of similarity to protein sequences in microbes depending of course on how you account for unique protein sequences. similarity to other species display a range of values for the same reason. If you don't include unique proteins with no corresponding function between the two species being compared then the percentage is high, but if you do include them the percentage can be much lower. The degree of similarity is also somewhat vaguely defined in that the cutoff for what constitutes similar is somewhat arbitrary. It is this similarity that leads to a conclusion by induction that gene sequences in humans have microbes as the original source.

[kitkat]

If you look at the research more closely what you will find is that by some percentage estimated between 10% and up to 90% of the expressed sequences that generate proteins share a degree of similarity to protein sequences in microbes depending of course on how you account for unique protein sequences. similarity to other species display a range of values for the same reason. If you don't include unique proteins with no corresponding function between the two species being compared then the percentage is high, but if you do include them the percentage can be much lower. The degree of similarity is also somewhat vaguely defined in that the cutoff for what constitutes similar is somewhat arbitrary. It is this similarity that leads to a conclusion by induction that gene sequences in humans have microbes as the original source.

 

Microbes as the original source but yet it believed right now that that only retroviruses can alter our DNA. Regardless the only real differences is that we have cells that can make tissue and organs where they don't have this ability or they never wanted it. The percentage is still higher with or without including unique proteins that currently have no corresponding function.

 

Considering that life arose by chance, it sure is a perfect system for the microbial community. This is evident in the fact that they have always been here.

[Fuzzwood]

Well, account for the fact that a lot of or cellular mechanisms do not differ much from microbial cell mechanisms and it will make sense that a lot of the "blueprint" should be the same too.

[cypress]

Considering that life arose by chance, it sure is a perfect system for the microbial community. This is evident in the fact that they have always been here.

 

Most origin of life researchers reject the notion that life arose by chance and for good reason too. The probability of deriving biologically relevant systems by chance processes is estimated in excess of 1 in 10^41,000 even by the more favorable chemic processes by numerous calculation methods, one of the more rigorous was by Sir Fred Hoyle. Current research is focused on self-assembly processes but thus far these are not faring any better.

 

Perhaps you meant to use the word "assuming" rather than "considering".

[CharonY]

And I suppose you do have good references for these assertions? I mean, ideally more than the opinion of an astronomist who has more than a fair share of controversial views?

[kitkat]

And I suppose you do have good references for these assertions? I mean, ideally more than the opinion of an astronomist who has more than a fair share of controversial views?

 

 

The bacteria bloom and implications of the Human Microbiome Project

 

Most origin of life researchers reject the notion that life arose by chance and for good reason too. The probability of deriving biologically relevant systems by chance processes is estimated in excess of 1 in 10^41,000 even by the more favorable chemic processes by numerous calculation methods, one of the more rigorous was by Sir Fred Hoyle. Current research is focused on self-assembly processes but thus far these are not faring any better.

 

Perhaps you meant to use the word "assuming" rather than "considering".

Right "assuming" at least that is what I am suppose to believe according to science.

 

More to the point, what is supposed to be "our" DNA. Gene sequences that are exclusively found in humans as compared to whom? Those are very little (if any). As we share common ancestries we share all the basic sequences with our relatives. The only genes that could be specific are those that arose after the last speciation event. But that was not that long ago and should account for a very little.

 

 

I see now I think what you saying is Our DNA carries the entire history since its origin and since no new species have come after us that is why it would be very little difference with all other life forms DNA.

 

Is this correct?

[Mr Skeptic]

Well, when we start designing our own life forms, then you can expect to find something that won't share half their genome with all other life.

[CharonY]

If we do, it will likely still be based on existing templates.

[cypress]

And I suppose you do have good references for these assertions? I mean, ideally more than the opinion of an astronomist who has more than a fair share of controversial views?

 

Good in the sense that alternative estimates are not clearly better. P.T. Mora a Research Biologist at the National Institute of Health provided a critique of the chance hypothesis for life from non-life back in the early sixties in published in Nature. That assessment was very similar to Hoyle's. In addition Robert Shapiro and Francis Crick accepted the probability of life by chance was effectively nill also. I find that those who suggest that life arose from non-life by chance are simply concealing an appeal to ignorance in a chance wrapper. If you believe I am wrong about this, by all means suggest a different number a we can discuss the relative merits.

 

Well, when we start designing our own life forms, then you can expect to find something that won't share half their genome with all other life.

 

Given the relative rarity of functional proteins, I would expect that very few of the genes in artificial life will be unique. I would expect that most will be reused from the pool of known and functional proteins.

[Mr Skeptic]

Given the relative rarity of functional proteins, I would expect that very few of the genes in artificial life will be unique. I would expect that most will be reused from the pool of known and functional proteins.

 

Yes especially at the start. But odds are it wouldn't fit on the phylogenetic tree -- we'd have no trouble mixing and matching proteins from distantly related species, like we do now adding Green Fluorescent Protein everywhere. And if projects like Folding@Home progress well, we can start designing our own proteins or optimizing existing ones.

[Sisyphus]

Who is suggesting that fully functional life as we know it would appear suddenly and spontaneously? Is that how you're interpreting "arise by chance?" The rise of life as we recognize the term would be a many step process, and those steps would not have to (and in fact probably could not) happen simultaneously. The "lightning hits bowl of goop" type origins of popular imagination and common straw man do not resemble anything scientists are actually investigating. The origin of life is still mysterious and hypotheses are incomplete, but such as they are they're a lot more plausible than that.

[cypress]

Who is suggesting that fully functional life as we know it would appear suddenly and spontaneously? Is that how you're interpreting "arise by chance?" The rise of life as we recognize the term would be a many step process, and those steps would not have to (and in fact probably could not) happen simultaneously. The "lightning hits bowl of goop" type origins of popular imagination and common straw man do not resemble anything scientists are actually investigating. The origin of life is still mysterious and hypotheses are incomplete, but such as they are they're a lot more plausible than that.

 

I don't know of any informed individual who makes the suggestion that life as we know it appeared suddenly by chance. I do know of many who suggest that random processes generated the first biologically active system we would describe as life-like and it is this suggestion I and the names I provided dismiss.

 

Yes especially at the start. But odds are it wouldn't fit on the phylogenetic tree -- we'd have no trouble mixing and matching proteins from distantly related species, like we do now adding Green Fluorescent Protein everywhere. And if projects like Folding@Home progress well, we can start designing our own proteins or optimizing existing ones.

 

An interesting aspect of proteins is that generally the primary sequence does not determine function, what generally does determine function is the shape and chemical and spacial affinities of key active areas (binding sites) of the protein.

[Sisyphus]

I don't know of any informed individual who makes the suggestion that life as we know it appeared suddenly by chance. I do know of many who suggest that random processes generated the first biologically active system we would describe as life-like and it is this suggestion I and the names I provided dismiss.

 

Is it? I thought you were talking about Fred Hoyle's analysis, i.e. "Hoyle's Fallacy." That is about specific complex structures arising by chance simultaneously.

[cypress]

Is it? I thought you were talking about Fred Hoyle's analysis, i.e. "Hoyle's Fallacy." That is about specific complex structures arising by chance simultaneously.

 

This is a different issue I think. You suggest that Hoyle's analysis is faulty simply because it uses analogous biological structures instead of actual ones because we lack the data required to use the structures that actually were involved in generation of the first biologically active self-generating system. Scientists use analogies all the time. Should we dismiss them because some people don't care for the analogies? It illustrates the point and it addresses one proposed mechanism directly. If you have a better set of components to illustrate the issue than the minimal set of proteins, lets have them.

 

While we are at it, let's make sure you are actually arguing a counter point rather than making an appeal to ignorance. Do you claim that there is a reasonable probability that life arose from non-life by random chemic processes alone?

[Sisyphus]

The problem isn't that it's an analogy, it's that it's a fallacious one.

 

And to answer your question, yes, I do think there is a "reasonable" probability, though treating the rise of life as one event and calling the processes "random" are both misleading. And no, I don't know exactly how it occurred. Nobody does. We have some plausible hypotheses about many of the steps. An appeal to ignorance would be suggesting that because we don't know what happened, X must have happened. I'm not doing that.

[CharonY]

Also functional proteins are not rare at all. Synthetic biology approaches demonstrated that synthetic peptides with more or less random elements of alpha and beta helices (IIRC) have the potential to catalyze simple reactions. Albeit with far lower efficiency than those that have arisen during evolution, of course. The existence of protein families and the prevalence of certain proteins is just another indicator of common evolutionary origins.

 

 

And as Sisyphus pointed out, no-one argues that there was just a random event and oops there is life. There must have been conditions that favored the existence of simple self-replicating biomolecules as a first step. Or maybe there were several first steps, so to say. Arguing from ignorance is not helpful.

Edited July 30, 2010 by CharonY

[cypress]

The problem isn't that it's an analogy, it's that it's a fallacious one.

 

And to answer your question, yes, I do think there is a "reasonable" probability, though treating the rise of life as one event and calling the processes "random" are both misleading.

 

Then you don't believe chance alone was involved and you would be hard pressed to make a case that the argument is fallacious because you reject the premise of chance alone. I don't see any reason to argue a point you don't accept in the first place. Hoyle's analysis applies to those who falsely stipulate chance alone.

 

And no, I don't know exactly how it occurred. Nobody does. We have some plausible hypotheses about many of the steps. An appeal to ignorance would be suggesting that because we don't know what happened, X must have happened. I'm not doing that.

 

No you reject the chance only hypothesis. my statement on an appeal to ignorance applies to those who pitch the chance only hypothesis.

 

Also functional proteins are not rare at all. Synthetic biology approaches demonstrated that synthetic peptides with more or less random elements of alpha and beta helices (IIRC) have the potential to catalyze simple reactions. Albeit with far lower efficiency than those that have arisen during evolution, of course. The existence of protein families and the prevalence of certain proteins is just another indicator of common evolutionary origins.

 

I find this argument to be very weak. One can use almost anyheavy solid that is denser than water for a boat anchor. Molecular biology confirms that the great majority of functional proteins are components of five or more multiprotein systems. Cherry picking exceptions does not impress me.

 

And as Sisyphus pointed out, no-one argues that there was just a random event and oops there is life. There must have been conditions that favored the existence of simple self-replicating biomolecules as a first step. Or maybe there were several first steps, so to say. Arguing from ignorance is not helpful.

 

I appreciate that you seem to be retracting your earlier implied argument about chance systems (where you took exception to Hoyle's indictment against chance alone) and have made clear you are with the rest of us who, like Hoyle reject that chance alone might have generated life from non-life.

Edited July 30, 2010 by cypress

[Sisyphus]

The problem is that it seems you're equivocating "chance" as in randomly picked from the set of all possibilities with "chance" as in the result of natural processes. Hoyle's Fallacy is a fallacy for that reason.

[Mr Skeptic]

Do you claim that there is a reasonable probability that life arose from non-life by random chemic processes alone?

 

I'd have to say yes, and furthermore that this chance is roughly the same as the chance that the universe is infinite (we don't yet know). But even with an infinite universe, it would be silly to expect to actually find an example of life arising by pure chance in a single step, rather than one via a several step process that includes chance and non-chance components.

[CharonY]

Molecular biology confirms that the great majority of functional proteins are components of five or more multiprotein systems. Cherry picking exceptions does not impress me.

 

So going back to irreducible complexity as an argument? You are aware that even for multienzyme (most prominently tryptophan synthase) complexes astonishingly still examples exist where there are stepwise changes in affinity of the subunits? That it is possible in a number of cases to trace down the development of such a complex into an operon? Do you really want to argue that everything we see now is just as it ever was and that the similarities and differences that are phylogentically traceable are just so designed?

Wow. The designer had a heck load of time on his hands.

 

 

The problem is that it seems you're equivocating "chance" as in randomly picked from the set of all possibilities with "chance" as in the result of natural processes. Hoyle's Fallacy is a fallacy for that reason.

 

Quoted for truth.

Edited July 30, 2010 by CharonY