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Theories - Origin of Life

Discussion of everything related to the Theory of Evolution.

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Re: Theories - Origin of Life

Postby scottie » Thu Jan 19, 2012 12:01 pm

Canalon
You are reading that HGT in Salmonella is under PhoP/PhoQ regulation, when what the paper you are citing is sating that the expression of (some of) the genes that get transfered in plasmids are under that regulation.

Of course it is an example. I used it to illustrate that HGT has to overcome a highly regulated response to any foreign transfer.
After all what is the purpose of the immune response system if it is not to protect against foreign ingress.
And HGT is extremely widespread and use a plethora of mechanisms that are not all regulated the same way (if at all).

I also stated that HGT is recognised only on the concept of similarity. But for it to be valid it has also to explain the mechanism.
Could you provide an example of a mechanism please. I don't know of one, maybe there is.
But please not an assumption, an actual mechanism by which this transfer has been shown to take place?
But no more than sex does HGT invlid the idea of common descent.

Common decent from what?
Please at least acknowledge that neo Darwinian theory is based on, not just common decent but on common decent from a Universal common ancestor. That is the foundation pillar of the theory, hence the tree of life concept. The hypothesis of HGT invalidates or at least challenges that concept.
That is what Koonin is showing.
As I understand it, you appear to be sliding away from that concept but at the same time arguing (as wbla3335 has) that there is no difference between the two views. There is a big difference.

Now of course sex produces a progeny from an ancestor but not from a Universal common ancestor.

We know that Darwin was wrong for the reasons you have given. But the standard theory, with all it’s epicycles, is what I am challenging.

but he is still right in the main idea (changes are generated and selected after generations).

With respect Patrick that is a very loose statement.
Changes are generated, but how?
Is not your view that these are random mutations (changes) to the genome.
Also
Can you also be clearer as to how these changes are selected after generations?
Philosophy is essential to science,

I agree but only within the bounds of what natural processes can demonstrate.
That is why the scientific method as a philosophical concept has stood the test of time.
It is also the reason I have, as you put it, wrapped myself into it.

The problem I have with “Darwinism or neo Darwinism or what is commonly referred to as evolution” is that it is philosophical view that attributes to natural forces that which these forces cannot accomplish, and I have been producing the evidence that demonstrates that point. Hence my often rather boring but I would argue detailed posts.

Any theory presented in broad terms can appear very persuasive, however it is in the details that it stands or falls.
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Postby JackBean » Thu Jan 19, 2012 1:22 pm

scottie, there is difference between lineage of genes and individuals. What we usually build from molecular data is gene tree, but does HGT affect the offspring production? I don't know how about you, but I could build my family tree, ergo I have a common ancestor.
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Re: Theories - Origin of Life

Postby wbla3335 » Thu Jan 19, 2012 2:14 pm

scottie

I think part of the problem with your posts is that you have difficulty communicating. You go on and on and on about this or that, but I, at least, have been unable to discern what your core arguments are (other than you think evolution is bogus). You could help us and yourself if you could focus. Maybe your ideas are clear in your head, but they are not in ours. I'll help by proposing that you complete the following sentence:

HGT disproves evolution (or common ancestry or whatever) because ________. (Notice the period at the end.)
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Re: Theories - Origin of Life

Postby scottie » Fri Jan 20, 2012 7:47 pm

I fully appreciate that there is often a communication problem here.

Jackbean
I understand the point you make about lineage and individuals. However the matter of HGT became relevant because when researchers tried to build gene tree lineages they hit a serious problem.
They started to get different results depending on which gene or indeed protein was being selected.
The problem was that one of their assumptions was that genes could only be handed down vertically ie from ancestor to offspring as per common decent and species divergence. (The Darwinian principle) the ultimate ancestor being (LUCA) in this bifurcating tree like process

The other assumption was that similar genes but in different species indicated common ancestry between species. The more similar, the closer the relationship on this bifurcating tree of life
So the theory was that a gene tree could be constructed showing the relationship between (and ultimately ) all species, thus proving Darwin’s idea, but through molecular investigation.

The problem that surfaced was that genetic information was found to be very intermixed even across domains.

Now this was initially showing up among prokaryotes (bacteria and archaebacteria)
But more recent research is revealing this showing even in eukaryotic life forms, as more animal genomes are sequenced. Evidence of this is the example of the Nematode that I have referred to.

So this similarity of genetic information has negated the original Darwinian tree.
What is now emerging is more like a bush or forest. Some even regard a Net to be a more accurate reflection of genetic history.

So Horizontal Gene Transfer is assumed to be the way in which this mix of genetic information has come about.

With all this in mind though, the actual mechanism(s) by which any transfer of genetic information between organisms takes place is unknown.

What is known is that any transfer that does take place must overcome the control and regulatory mechanisms that prevents foreign genetic mixing.
These controls present a serious challenge to genetic transfer because the controls are specifically intended to prevent such transfers.
When that does happen it is invariably deleterious to the receiving organism.

The only mechanisms that I am aware of is that which researchers use in the labs.
Of course these is not natural but artificial mechanisms

So wbla3335 coming to your question

HGT disproves evolution (or common ancestry or whatever) because ________. (Notice the period at the end.)

HGT does not disprove the “evolutionary” ie the change over time, view.

If such mechanism(s) of this transfer actually exist, as they are assumed to, then it is a serious challenge to the view of common decent from a universal common ancestor. This of course is the Darwinian core concept and it is what Koonin was explaining.
Koonin does of course assume that mechanisms do in fact exist, we just haven’t discovered them yet.

Remember though, that it is the similarity of genetic information in different species that has led to the assumption that transfers have taken place.
I see a more appropriate name for this observation to be Horizontal Gene Similarity as opposed to “Transfer”, unless of course an actual natural mechanism is discovered.

The design view such as I advocate, would argue that this similarity is evidence of a natural way for a designer to reuse different functions already designed, in different species, with slight modifications to suit the particular circumstances.
GM crops is a practical example of how this is achieved.

Gene therapy is also another design applied way to rectify faulty mechanisms, but with significantly high risks to organs when natural immune responses are suppressed to allow these modifications.

Gene similarity across even distant species challenges the core Darwinian principle of common ancestry.
If there is a natural mechanism for HGT then certainly the core pillar of universal common decent is refuted.
However it does not refute evolution (i.e change over time) as such.
I hope this clears up any misunderstandings.
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Re: Theories - Origin of Life

Postby wbla3335 » Sat Jan 21, 2012 3:22 am

scottie wrote:Gene similarity across even distant species challenges the core Darwinian principle of common ancestry.
If there is a natural mechanism for HGT then certainly the core pillar of universal common decent is refuted.

Are you saying that HGT discredits phylogenies derived from vertical transmission? If so, you are really grasping at straws. Do you really think that an omnipotent creator would need to reuse gene sequences here and there? Why bother to create a huge diversity of gene sequences in a huge diversity of creatures and then get lazy with a relative few? Saying that HGT refutes common descent is like saying that the similarity of a few gene sequences in diverse organisms refutes the existence of an omnipotent creator.
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Re: Theories - Origin of Life

Postby scottie » Tue Jan 24, 2012 1:46 pm

wbla3335
Sorry for the delay. Life beyond this forum exists. :)
Now I do wish you would respond to what I actually write.
This is what I wrote
However the matter of HGT became relevant because when researchers tried to build gene tree lineages they hit a serious problem.
They started to get different results depending on which gene or indeed protein was being selected.


Is it your claim that that these problems are not manifest?

This hypothesis was introduced, essentially by Gogarten and Woese, to explain these very difficulties.

If they didn’t exist, HGT would not have been a necessary hypothesis
So is there vertical lineage?
Yes, within species.
Are there problems in determining what the vertical lineage actually is beyond species?
Again Yes.
Why?
Because when researchers try to establish these lineages they get different results depending on which gene or protein they use.
Hence the concept of HGT was formulated to explain away these difficulties.

So is the hypothesis of decent from a common universal ancester correct?

Well it can only be regarded as correct if it can be demonstrated to be so.
Molecular investigation was the mechanism that was expected to do just that.
Although very informative it has not shown that vertical decent from a Universal common ancestor (i.e. across species) is correct.
Do you really think that an omnipotent creator would need to reuse gene sequences here and there?

Why not?
This principle is sound in design theory.
Designers follow this principle every day in their design works.
How many different versions of the wheel do you see in designs today and indeed throughout history.
What about sub routines in computer programming?
Many of these routines are called upon variously and in different programs.
The very computer application you are using to communicate your views on this forum is replete with routines used commonly.

Saying that HGT refutes common descent is like saying that the similarity of a few gene sequences in diverse organisms refutes the existence of an omnipotent creator

I don’t understand what it is you are trying to say.

What I will do however is ask you a simple question.

What challenges have to be overcome for HGT to actually occur in nature.
In other words, for DNA to be taken up from another organism, what stages of transfer would be required from both donor and recipient.
You are a biologist so you should have no difficulty in explaining to this forum what those stages would be.
Would you do that, please.

If you are unable to then I would be quite happy to do so.
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Re: Theories - Origin of Life

Postby JackBean » Tue Jan 24, 2012 4:10 pm

Are there problems in determining what the vertical lineage actually is beyond species?
Again Yes.
Why?
Because when researchers try to establish these lineages they get different results depending on which gene or protein they use.
Hence the concept of HGT was formulated to explain away these difficulties.


That's why I was talking about the difference in gene and individual trees. You should know, that even creation of the gene trees is little magic simply because we do not know when and what changes happened. We are usually going for least changes, but there is a chance that some mutation occurred and then other, reverting one occurred again.
But since we are able to build trees of individuals, we would be theoretically trace our ancestors down to LUCA.
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Re: Theories - Origin of Life

Postby wbla3335 » Wed Jan 25, 2012 4:34 am

scottie wrote:However the matter of HGT became relevant because when researchers tried to build gene tree lineages they hit a serious problem.
They started to get different results depending on which gene or indeed protein was being selected.

This happens without HGT.

Is it your claim that that these problems are not manifest?

No.

This hypothesis was introduced, essentially by Gogarten and Woese, to explain these very difficulties.

If they didn’t exist, HGT would not have been a necessary hypothesis

HGT was known long before anyone tried to build trees from sequences. HGT is only one of the problems phylogeneticists face.

Because when researchers try to establish these lineages they get different results depending on which gene or protein they use.

This happens without HGT sequences. See above. Phylogenetics is a complicated endeavour that requires a very careful selection of sequences.

Hence the concept of HGT was formulated to explain away these difficulties.

Still wrong. HGT was formulated to explain the existence of identical or nearly identical sequences in organisms too diverse for the sequences to have got there vertically. "Explaining away" is your interpretation.

Do you really think that an omnipotent creator would need to reuse gene sequences here and there?
Why not?

Agree. Since you are designing your designer, you can give it whatever properties you wish.

I don’t understand what it is you are trying to say.

The occurrence of identical or nearly identical sequences in a diverse array of organisms clearly falsifies creation.

What challenges have to be overcome for HGT to actually occur in nature.
In other words, for DNA to be taken up from another organism, what stages of transfer would be required from both donor and recipient.
You are a biologist so you should have no difficulty in explaining to this forum what those stages would be.

I'm not unable, but as I've said, I'm not here to educate you. Your postings aren't worth so much of my time.
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Re: Theories - Origin of Life

Postby scottie » Fri Jan 27, 2012 12:35 pm

wbla3335
I'm not unable, but as I've said, I'm not here to educate you. Your postings aren't worth so much of my time.


I take it then that you don’t actually understand the intricacies of the HGT proposal OR you do understand, but can’t bring yourself to openly acknowledge what prevent this as a viable explanation.
So allow me to set out the problems and I will do that next.

Jackbean
I think we are getting onto the same page here.
As you say even the building of gene trees is a little magic because we don’t know when and what changes happened.
How true.
If we don’t know or even understand what those basic fundamentals are, how can we then say these evolutionary forces are matters of fact.
I acknowledge of course that you are not saying that but others are doing just that.
But since we are able to build trees of individuals, we would be theoretically trace our ancestors down to LUCA.


But these gene trees can only be established within species.
To theoretically trace back to LUCA HGT must be invoked.
The question is how valid a hypothesis is HGT?

That is what wbla3335 is having difficulty in coming to terms with.
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Re: Theories - Origin of Life

Postby scottie » Fri Jan 27, 2012 12:48 pm

Here are some of the stages whereby a cell can take in foreign DNA.
1 There has to be DNA in the immediate environment.
2 The host cell must be capable of receiving this DNA. In other words it
must be competent, which begs the question, what is competence?
3 For any interaction between the cell and free DNA, specific sequences
and receptors are involved..
4 How is the entry of DNA through the outer cell membrane (periplasmic
space) and then, in the case of eukaryotic cells, the nuclear
(cytoplasmic) membrane processed.
5 This foreign DNA then has to be integrated into the chromosome so that
it can be functionally expressed into cell operation.
Apart from the first all these stages are common to any type of gene transfer.

So by simply enumerating the stages we begin to get an idea of what any natural and unguided process has to produce.

But of course it becomes much more complicated when we start to investigate each stage process. Lets just touch on some of the detail.

Stage 1 It is assumed that DNA in varying concentrations is present in almost any environment, due to spontaneous cell lysis (breakdown), digestion etc.

Stage 2. Competence
This is a specific physical state of bacterial cells that allows nucleic acids to bind to the cell surface and be taken up by the host.
Studies have shown that are different requirements for different lengths of this free DNA, also for different states of DNA, i.e ssdna (single stranded) dsdna (double stranded) If you look up any review on this matter of competence you will invariable find such expressions as “unclear” “not known” even “mysterious”.
Some research suggests that only about 1% of bacterial species are naturally capable of taking up DNA under lab conditions.

Stage 3 requires specific molecules to be in place. How? from where?

Stage 4 So how does this transfer occur. Well the simple answer is we don’t know.
What we do know however is what kinetic studies have shown and that is, the process of transfer through just the nuclear(cytoplasmic)membrane occurs surprisingly, quite rapidly. Surprising because this is a very highly controlled and regulated process with very defined energy requirements.

Stage 5 This DNA has then to be functionally integrated into the host chromosome, again another highly controlled and regulated process. Remember the host cell naturally guards against foreign infestation.

The details of each stage would require it’s own essay in explanation apart from all the unknowns.
So just a very brief overview of a process reveals what is naturally possible and what is not.
HGT is a hypothesis that has been posited to try and explain away the incongruities between the Darwinian species tree founded on LUCA and what gene trees are revealing.
But as we can see from just this simple overview even this process cannot be accommodated within the framework of natural and undirected processes.
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Re: Theories - Origin of Life

Postby wbla3335 » Fri Jan 27, 2012 7:56 pm

Just a few things for you to ponder and look into, scottie.

Do you consider HGT by your proposed "steps" impossible or unlikely?
Research other proposed mechanisms.
Investigate the difference between gene trees and species trees.
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Re: Theories - Origin of Life

Postby scottie » Sat Jan 28, 2012 2:54 pm

wbla3335
Oh dear, I am going to try and be patent

Do you consider HGT by your proposed "steps" impossible or unlikely?

These aren’t my proposed steps. These are the steps required to effect gene transfer. There is clearly a gap in your understanding of the process.

Do you consider HGT by your proposed "steps" impossible or unlikely?

HGT is a reality, in the laboratory of researchers that design the methodology required. GM in crops is one such process.
In nature it is assumed because of the similarity of gene sequences in different species.
Do please try and at least understand the subject you are cat calling about.

Research other proposed mechanisms.

What other mechanisms?
Or are you going to revert to your “ It is not my job to educate you” mode :)

Investigate the difference between gene trees and species trees.

Are you not aware that the molecular investigation of genes was intended to support the Darwinian species tree concept of vertical inheritance that provided speciation?
Therefore the gene tree was supposed to confirm the Darwinian tree of life concept.
It hasn’t proved to be so and that is why the concept of HGT has been proposed.
Now what is it you seem to be finding so hard to grasp?
You are clearly out of your depth here, my advice is to stop digging, the hole is getting rather large.
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