Theories - Origin of Life

[scottie]

Horizontal Gene Transfer and the Tree of Life
A common premise of all molecular phylogenetic methods is that genes are transmitted via vertical, lineal inheritance, i.e. from ancestor to descendant.

It was anticipated that this method would demonstrate the Darwinisn mechanism of common decent, and the universal tree of life would be vindicated.

However these molecular comparisons began producing some very contradictory results.
The hoped for Darwinian Tree of Life (TOL) simply has turned out to be more of a bush or even forest.

The largest biomedical research facility in the world is the National Institutes of Health with its subdivisions, National Center for Biotechnology Information, National Library of Medicine, at Bethesda, MD USA.

This is what Eugene Koonin it’s Senior Investigator along with colleges presented in their paper in 2001

http://www.ncbi.nlm.nih.gov/books/NBK2228/
Horizontal Gene Transfer in Prokaryotes: Quantification and Classification
Eugene V. Koonin,1 Kira S. Makarova,1,2 and L. Aravind2.
Annu. Rev. Microbiol. 2001. 55:709 – 42.

Horizontal (lateral) gene transfer, the transfer of genes between different species, is an evolutionary phenomenon whose extent and even very existence have been the subject of a longtime debate that tends to become particularly vigorous when cases of horizontal gene transfer that involve eukaryotes are considered (98, 103). This is understandable because (a) horizontal gene transfer seems to challenge the traditional, tree-based view of the evolution of life and the core neo-Darwinist belief in the central role of reproductive isolation between species in evolution (21–23, 53, 74, 89, 90) concepts that, at least initially, have been developed in studies on the evolution of sexually reproducing eukaryotes, and (b) like many evolutionary phenomena, horizontal transfer is hard to prove unambiguously.

Eight years later and as a result of more accumulated evidence Koonin and colleges present some more findings.

http://www.ncbi.nlm.nih.gov/pubmed/19594957
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. (2009)
Puigbò P, Wolf YI, Koonin EV.

CONCLUSIONS:
Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.

So lets try and bring this up to date.
A team of researchers has attempted to produce a new model of decent.
They have termed it the “Rooted Nest of Life”.
http://www.ncbi.nlm.nih.gov/pmc/article ... ool=pubmed
A Rooted Net of Life 2011
David Williams, #1 Gregory P Fournier, #2 Pascal Lapierre,3Kristen S Swithers,1 Anna G Green,1 Cheryl P Andam,1 and J Peter Gogarten 1

All papers are reviewed by expert reviewers before publication
Reviewer 1: W. Ford Doolittle, Dalhousie University Comments ( He is regarded as one of the foremost researchers in this field. Here is an extract of his comments.

Reviewer 1 continued: Second, we might ask why the microbial systematics and evolution community still feels that we need some single way of describing the relationships of organisms and some singly historical "metanarrative" to undergird it. I'd guess our colleagues doing human linguistic, cultural and social history would see this as an unnecessarily simplistic and ultimately misleading aspiration (see for instance [95]). Is it just our need to defend Darwinism from its politically powerful opponents that causes us to cling to it?

Authors' response: This is a fascinating question. In the context of this manuscript, we make the assumption that there is a single "true" sequence of events or organization of matter on the temporal and spatial biological scale (i.e., Life on Earth). The goal of reconstructing the resulting relationships between organisms is therefore to recover a single, historical description - but any such attempts are limited by the methods used and the data available (which at present do impose limitations on the confidence of historical events/relationships).

Reviewer 2 continued: Eric Bapteste, Université Pierre et Marie Curie
The authors suggest that rooting the ribosomal tree of life should help by polarizing the complex reticulations of the many gene trees mapped onto it. This seems optimistic: individual gene phylogenies can be so messy (due to duplication, losses, and recombinational lateral gene transfer in addition to speciation) that even knowing how to root the ribosomal tree may not be that decisive for the polarization of these gene trees.

Authors' response: We agree that mapping a gene tree onto the ribosomal scaffold is a complex, non-trivial process that needs to consider probabilities of gene duplications, gene loss, and gene transfer. Certainly, mapping a gene with sporadic disjoint distribution will need to incorporate gene transfer relative to the ribosomal scaffold. Furthermore, the comment on messiness is entirely correct. In many instances multiple mappings are possible, especially if extinct and unsampled lineages are taken into consideration. Especially for small gene families the distinction between gene-transfer donor and recipient often is not possible. The identification of donors and recipients is certainly probabilistic and not absolute. However, these limitations not withstanding, the availability of a rooted reference tree greatly facilitates the integration between gene and reference tree

There is a lot more but is this not enough to sum up the case against TOL.
But what about the “messy bit” Horizontal Gene Transfer.
Well lets keep that for the next post as this one is probably long enough.

[JackBean]

So? How does horizontal gene transfer in bacteria disproof evolution (in eukaryotes)?

[scottie]

JackBean

So? How does horizontal gene transfer in bacteria disproof evolution (in eukaryotes)?

The hypothesis of HGT militates against common decent and therefore the tree of life concept as posited by Darwin and also the neo Darwinian synthesis.

This is why there is such a vigorous debate between the opposing views within the evolutionary community, hence Koonin et al’s observation that I quoted.

“horizontal gene transfer seems to challenge the traditional, tree-based view of the evolution of life and the core neo-Darwinist belief in the central role of reproductive isolation between species in evolution”

And HGT is the hypothesis that is intended to explain the reason why molecular phylogenetic trees produce such contradictory results.

HGT doesn't disprove any evolutionary process. It disproves the core Darwinian concept of decent from a universal common ancestor.

Please remember the phylogenetic tree was intended to prove common decent from a universal common ancestor and the tree of life diagram has been used to explain the common and vertical inheritance from that ancestor.

I hope I have explained that more clearly.

However the HGT has it’s own difficulties as well as I hope to show next.

[wbla3335]

Scottie

Few, if any, evolutionary biologists deny that HGT complicates the construction of prokaryotic trees. I doubt that any evolutionary biologist would consider this a problem for evolutionary theory. You contend that anything other than a simple, unambiguous, linear tree of life disproves evolution. No one educated in the biological sciences would make such a contention. When I looked at the parts of the quotes that you have put in bold in your posts, it became very clear that you do not understand what these people are saying. They are saying that evolutionary history is complex, not that it is wrong. As Jack has urged, please clarify why you think that HGT falsifies evolutionary theory. Specifically, please provide support that these authors, particularly Koonin, think evolution is bogus. You should thoroughly research something before misrepresenting quotes. Science, which you claim to admire, does not tolerate poor research.

[scottie]

wbla3335 » Sun Jan 15, 2012 5:15 am

As Jack has urged, please clarify why you think that HGT falsifies evolutionary theory

Please read what I have actually said or have you not bothered to read my response to Jackbean’s question.
You don’t have to look very far, just 7 lines from the bottom of my last post.

HGT doesn't disprove any evolutionary process. It disproves the core Darwinian concept of decent from a universal common ancestor.

Does that sound as if I am claiming HGT is falsifying evolutionary theory?

It is militating against the core Darwinian view of common ancestry.
Koonin actually goes further than I have. He includes the

central role of reproductive isolation between species in evolution

Please argue against what I am actually saying.

Specifically, please provide support that these authors, particularly Koonin, think evolution is bogus. You should thoroughly research something before misrepresenting quotes. Science, which you claim to admire, does not tolerate poor research.

Once again where have I stated that Koonin thinks evolution is bogus?
Are you not aware that I also acknowledge that evolution actually happens.
Change over time is a fact of life.
It is the Darwinian process of random mutation and speciation that I challenge, and I bring to bear the research of major figures and institutions of science in support.

So please when it comes to misrepresenting views it would be helpful to follow your own advice.

[wbla3335]

HGT doesn't disprove any evolutionary process. It disproves the core Darwinian concept of decent from a universal common ancestor.

The conjunction of these two sentences belies your level of understanding. Evolution IS descent from common ancestors. You're suggesting that HGT disproves this. It doesn't. Are you suggesting that HGT is the dominant means of gene transfer? Are you suggesting that HGT somehow negates the consequences of vertical transfer?

It is the Darwinian process of random mutation and speciation that I challenge, and I bring to bear the research of major figures and institutions of science in support.

You have done no such thing. You have misunderstood, quoted out of context, and promoted minority views while ignoring the overwhelming evidence that does not support your faith.

[scottie]

wbla3335

"scottie wrote:HGT doesn't disprove any evolutionary process. It disproves the core Darwinian concept of decent from a universal common ancestor."

The conjunction of these two sentences belies your level of understanding. Evolution IS descent from common ancestors

(1) Darwinism and neo Darwin or Modern synthesis IS decent from a Universal Common Ancester.(LUCA) not the rather loose description you appear to be trying to slide into.
Unless, -- if you are advancing your own private theory then please clearly state what that theory is so there can be no confusion.

You're suggesting that HGT disproves this. It doesn't.

(2) Doesn’t disprove what? Your private theory or the neo Darwinist belief?
Koonin’s view is

horizontal gene transfer seems to challenge the traditional, tree-based view of the evolution of life and the core neo-Darwinist belief in the central role of reproductive isolation between species in evolution.

Is he wrong?
If so then may I suggest that you inform Koonin of that fact and perhaps demonstrate it by presenting your evidence in support. (so far you are simply making statements

Are you suggesting that HGT is the dominant means of gene transfer?

No

Are you suggesting that HGT somehow negates the consequences of vertical transfer?

Again No – vertical transfer is a fact of inheritance. Why would you think I was suggesting that?

Maybe when I actually get to the point of presenting the evidence relating to HGT that researchers are bringing to light you may understand the subject a little bit more.

Now finally

"It is the Darwinian process of random mutation and speciation that I challenge, and I bring to bear the research of major figures and institutions of science in support."

You have done no such thing. You have misunderstood, quoted out of context, and promoted minority views while ignoring the overwhelming evidence that does not support your faith.

If I have done no such thing. Well then please explain what else you require in the way of evidence.
For example
When I refer to NASA’s considered view that I reported in this post
about14351-180.html
by scottie » Fri Aug 19, 2011 12:31 pm
This is a minority view is it?
Or when I reported on the evidence of no precursor to the ribosome here
about14351-204.html
by scottie » Tue Sep 13, 2011 10:05 pm
This is something being taken out of context is it?
Or when I reported on the subject of cave animals here
about14351-384.html
by scottie » Sun Dec 25, 2011 1:01 pm
What just another minority view?

When I reported on isochores here
about14351-396.html
scottie » Tue Jan 03, 2012 12:15 pm
Of course another minority view. Why should anyone pay attention to the NIH?

If all this evidence is wrong then you should have no trouble in refuting them with your own evidence.
I don't understand why you are so reluctant.
Could the uncomfortable truth be that you are simply unable to.
That would be an explanation, would it not?

[JackBean]

Are you suggesting that HGT is the dominant means of gene transfer?

No

Are you suggesting that HGT somehow negates the consequences of vertical transfer?

Again No – vertical transfer is a fact of inheritance. Why would you think I was suggesting that?

Because if no, there is no problem. For the vertebrates you can easily make a tree of life with only one ancestor. For previous life it will be little bit harder, since it's more like bush than tree, but it would lead to one single ancestor again.

[wbla3335]

Darwinism and neo Darwin or Modern synthesis IS decent from a Universal Common Ancester

Isn't that what I said?

Doesn’t disprove what?

What you were claiming it disproves.

Is he wrong?
If so then may I suggest that you inform Koonin of that fact

Koonin knows exactly what he is saying (and why). You don't.

Maybe when I actually get to the point of presenting the evidence relating to HGT that researchers are bringing to light you may understand the subject a little bit more.

I've been interested in HGT since it first came to light. Do you really think your armchair understanding of anything biological surpasses that of biologists? Didn't you say you were some sort of engineer? I'm an armchair physicist and would never have the audacity to suggest that I know more than a real physicist. Get real.

I don't understand why you are so reluctant.

It's not my part to educate you. The biologists on this forum enjoy answering legitimate questions, but we are not compelled to cater to deniers. When anti-evolutionists come onto an evolution forum, the onus is on them to convince us, not for us to convince you. You're not looking for answers. You're not making much progress here, partly because you're not presenting a coherent argument, and partly because you interpret your "evidence" through the filter of your faith. Science requires an open mind and a willingness to weigh ALL the evidence.

[scottie]

Here is a Primer in HGT
Now stick with this, it is not coming from an armchair biologist, you will find this journal helpful

http://www.landesbioscience.com/journal ... cle/18776/
What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals

Definition

Horizontal gene transfer (HGT) can be defined as the movement of a gene from one donor species to a receiver species by means other than vertical inheritance from a direct common ancestor has been recognized as an important phenomenon in the evolutionary biology of prokaryotes.

It continues

In eukaryotes, in contrast, the importance of HGT has long been overlooked and its evolutionary significance has been considered to be mostly negligible. However, a series of genome analyses has now shown that HGT not only do probably occur at a higher frequency than originally thought in eukaryotes but recent examples have also shown that they have been subject to natural selection, thus suggesting a significant role in the evolutionary history of the receiver species.

So what is the mechanism that effects this transfer?
It continues
How Were the Genes Transferred in Nematode Genomes?

Both for plant-parasitic and necromenic nematodes, the question of the mechanisms that have allowed successful gene transfer in their genomes is intriguing and remains undetermined. Intuitively, gene transfer in the genome of an animal appears very challenging. Indeed, even if we assume that the gene is transferred in a genomic location compatible with its transcription and translation, several barriers have to be passed before a gene can be integrated in the genome of an animal. Animals have a separate germline and HGT must reach cells in the germline to have a chance to be transmitted to the offspring, otherwise they will remain individual-specific….

Conclusion
As more animal genomes are being sequenced we can expect new cases of HGT to be reported. Usually, candidate HGT in animal genomes are identified by searching genes that are more similar to bacterial or fungal genes than to genes of closer relatives like other animals. However these approaches will not allow identifying HGT events between different animals.

So although HGT is being more and more recognised as having occurred in eukaryotes, the mechanism of this gene transfer is undetermined. The way HGT is recognised is by gene similarity.
The assumption being that this sort of similarity has come about by as yet some unknown evolutionary process.

So what would any evolutionary process have to take account of?
Again lets not speculate

Here is some interesting information of immune system response to gene alterations from the Stanford School of Medicine.
How does HGT invade a cell without the immune system responding to prevent?

http://med.stanford.edu/news_releases/2 ... quirt.html
This interesting article on sea squirts shows that Sea squirts only fuse with relatives (genetically similar). It rejects those that are not near relatives.

So, a reasonable question
How does HGT take place without immune response, especially in nature?
Has HGT ever been observed or is it just a hypothesis to explain gene similarity in different species.

What is research actually revealing?
Lets go to this paper

Lateral gene transfer and the nature of bacterial innovation
http://www2.yale.edu/ochman/Papers/Ochm ... re2000.pdf
Under the subheading

The impact of acquired DNA (page 303)
Lateral gene transfer provides a venue for bacterial diversification by the reassortment of existing capabilities. Yet, while the emergence of new phenotypic properties through lateral gene transfer furnishes several advantages, it also presents several problems to an organism.
Newly acquired sequences, especially those conferring traits essential to only a portion of the bacterial life cycle, are most useful when they are appropriately and coordinately regulated with the rest of the genome.
In Salmonella, the expression of several independently acquired virulence genes is under the control of a single regulatory system - the PhoP/PhoQ two-component system that was already performing essential functions in the genome before the acquisition of these genes
Although the precise manner by which each of these genes is regulated has yet to be resolved, these findings suggest that the physiological capabilities and adaptation of very divergent bacteria rely on a common set of universally distributed regulatory signals

HGT therefore has to be a highly regulated process

So what is PhoP/PhoQ regulation?
Here is a good description of this regulation
http://jb.asm.org/content/183/6/1835.full

The Pleiotropic Two-Component Regulatory System PhoP-PhoQ
Here, I first discuss how the PhoP-PhoQ two-component system responds to environmental cues and interacts with other regulatory systems to integrate multiple signals into a coordinated cellular response and then I describe the PhoP-regulated genes mediating the various PhoP-controlled functions, including virulence.

The phoPQ operon is autogenously controlled, that is
Regulation of gene expression is by a product of the gene itself that either inhibits or enhances the gene's activity.


A bit more information from
Proceedings from The National Academy of sciences of the United States

Autogenous and nonautogenous control of response in a genetic network
http://www.pnas.org/content/103/34/12718.full

Discussion
Biomolecular interactions within cells ultimately decide their physiology. This genetic circuitry resembles in many aspects that found in other nonbiological scenarios, and thus control ideas commonly used in these contexts have been incorporated into the understanding of cellular action (30).
These types of studies are contributing to the discovery of a set of feedback-based regulatory strategies in biological systems and to further confirmation of the possible identification of fundamental design principles of cellular control [e.g., robustness (5, 6), noise tolerance (7), programmed temporal order (8, 11), sign-sensitive dynamics (9, 10), ultrasensitivity (12), optimal performance (13), and implementation-dependent dynamics (14)].

Pay particular note to the acknowledgement of “fundamental design principles of cellular control”

Why is this control and regulation needed?

Well let the Institute of Science in Society answer that question
http://www.i-sis.org.uk/FSAopenmeeting.php

Recent Evidence Confirms Risks of Horizontal Gene Transfer

Horizontal gene transfer is one of the most serious, if not the most serious hazard of transgenic technology. I have been drawing our regulators’ attention to it at least since 1996 [1], when there was already sufficient evidence to suggest that transgenic DNA in GM crops and products can spread by being taken up directly by viruses and bacteria as well as plant and animals cells….

Also check out Gene therapy from Human Genome Project Site
http://www.ornl.gov/sci/techresources/H ... rapy.shtml

Now if you really want to believe that all this level of cellular control, (and here I have only touched on one little area of cellular organism,) is the product of random and undirected happenings, then your faith in miracles seems to have no bounds.

This is evidence of design at it’s most exquisite, and even the proceedings from the National Academy of Sciences has no difficulty in openly acknowledging this.

So please, unless you can demonstrate how your random and undirected happenings can produce all of this, then you have no case to defend.

Richard Dawkin’s get out of jail phrase is that “science is working on it”
Is that your answer?
Oh and by the way he (Dawkins) has recently announced that he has retired from the field of Public understanding of Science. Can’t say I am surprised.

[wbla3335]

scottie, how does ANY of this disprove evolution (or common ancestry or whatever)?

[canalon]

Or even correct understanding of what is read for that matter.
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. That is quite different.
And HGT is extremely widespread and use a plethora of mechanisms that are not all regulated the same way (if at all). But no more than sex does HGT invlid the idea of common descent.

And by the way, if you aim to discredit Darwin's explanation of the mechanism of evolution, you are wasting your time. Everybody knows he was wrong in the details (how else, he had no ideas about genes and such), but he is still right in the main idea (changes are generated and selected after generations).

And as a parting remark, your attacks against what you call philosophy are again underlining your lack of both understanding of science and selfawareness. Philosophy is essential to science, it is the reflection about our practices and how we go on about doing science. There is a lot of useless fluff, but a lot of it is useful. Just like the scientific method that you like to wrap yourself into. It is essentialy a philosophical description of what science is and how it should work.