Theories - Origin of Life

[scottie]

Gavin

The goal posts are already philosophical. I haven't moved them.

You have said it all.
Evolutionary theory is philosophical, which is what I have always been saying.

This thread is about scientific theories of Origin, and I am arguing that Darwinian theory is not backed up with scientific evidence. It is supported by a philosophy.
I am providing evidence that backs up my claim and you respond that I am being selective in presenting the evidence.

If I am selective, then please present the evidence that opposes my understanding, but not with vague statements like “ the weight of evidence” or

“Ignoring the myriad of trees that have been built from the available evidence is an example of how you are selectively discounting the available evidence that doesn't support your beliefs”

If this evidence is based on science and not philosophy then it can be examined scientifically for its veracity.

So why don’t you just produce a phylogenetic tree and lets examine it scientifically.
Just one other point

Every one is aware that functional design (whether good, or not so good or even downright bad) displays itself with certain properties.
1) The function has a purpose. ( i.e. It goes from A to B with C as it’s goal )
2) Method by which that purpose is achieved. (How does it go from A to B)
3) It would not contain parts or units that had no function toward the purpose.

Why should these properties be limited to design?

Gavin, you are arguing against yourself now.
How on earth can a process on the one hand be random and undirected and at the same time be purposeful?

I think it was Jerry Coyne who said that he would abandon his belief in evolution if a human fossil were ever found in Cretaceous strata.

Jerry Coyne is on a pretty safe bet here.
Even many Creationists would go along with that one
Oh and I would be quite happy to examine the contradictions and circular arguments in his book "Why evolution is true." at another time.

Now I am not looking for answers to these ones just making the point.

However can we just concentrate on an example of a phylogenetic tree so we can discuss it scientifically.

Please don’t feel you have to rush a response, just carefully choose an example and cover all the angles you can think of.
I say this because I do sincerely have respect for your views even though we part company on some.

In the meantime I will present some more evidence to ponder on.
This time it covers the whole structure of a genome and the evidence that has emerged.

[scottie]

Gavin Here is some more evidence, this time on Isochores
Erwin Chargaff identified two Rules governing DNA.
The first which gave Watson and Crick the necessary leg-up in identifying the structure of DNA.
These 4 nucleotide bases are Adenine (A), Thymine (T), Cytosine (C), Guarnine (G)
Chargaffs Rules govern two things.

1) Adenine(T) always pairs with Thymine (T) and are in equal amounts
Guanine (G) and Cytosine (C) always paired and are in equal amounts.
2) The ratio of the amounts (G+C) and (A+T) varies from species to Species and is universal. (Chargaff's C+G% rule)
In other words this ratio is species specific.

There are large regions of DNA (greater than 300 KB) with a high degree uniformity in G-C and C-G (collectively GC) and these regions tend to have more genes, and important genome features are dependent on these isochore regions or structures, e.g. genes are found predominantly in the GC-richest isochore classes.
http://www.ncbi.nlm.nih.gov/pubmed/11591471

Here is an abstract from a paper that emphasises importance of these isochore structures.
http://www.ncbi.nlm.nih.gov/pubmed/11433361 2001

Abstract
One of the most striking features of mammalian chromosomes is the variation in G+C content that occurs over scales of hundreds of kilobases to megabases, the so-called 'isochore' structure of the human genome. This variation in base composition affects both coding and non-coding sequences and seems to reflect a fundamental level of genome organization. However, although we have known about isochores for over 25 years, we still have a poor understanding of why they exist.

So an outstanding feature of eukaryote genomes is this segmentation of the DNA into these isochore regions, each with a distinctive species specific base composition.

Therefore to view the genome without reference to it’s isochore mosaic would be like describing, say, the Colorado River without any reference to the Grand Canyon, or the Grand Canyon National Park, Colorado desert or Horseshoe bend etc etc, the very structures that guide and direct the river to its destination into the gulf of California.

However the fact is that most of us view the genome in precisely this manner.
This means that although we acknowledge the fact of the genetic code, (how did that come about I wonder) we almost always are oblivious to this other level of information that organises the genome, and another thing, remember also that each genome organisation is species specific.

If a graph is drawn of the relative densities of GC we would get an undulating line of hills and valleys, with the gene distribution being mainly around the hill sections of the genome

This type of graph is precisely what the authors of a paper appearing in Nature plotted.
The paper is entitled
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Rat Genome Sequencing Project Consortium*
*Lists of participants and affiliations appear at the end of the paper
http://www.nature.com/nature/journal/v4 ... e02426.pdf.
The principle author of this paper is Francis Collins,.along with some 150 or so other researchers.( I stopped counting after about 100)

Now why is this significant as far a evolutionary theory is concerned.?
Because it reaches directly into the issue of Darwinian speciation.

If you bring up the paper in a separate tab and scroll down to page 502 of this paper you will notice 4 graphs in figure 9

Let just examine the graph 9c labelled “Lineage specific SINE content”
The X axis represents some 110 million base pair segment of the Rat chromosome 10.
The Y axis Red line represents the Rat specific SINE distribution.
The Green line represents the corresponding distribution in the Mouse genome.
It is quite noticeable that the two demonstrate a remarkable similarity. In fact it could be argued that one is a copy of the other with a few minor amendments.

Each graph denotes only lineage specific mutational insertions affecting mostly the so called Junk DNA.
Now here is the rub.
Evolutionary theory posits that the Rat and Mouse diverged from a common ancestor some 20 odd millions years ago.

So what we are seeing are two independent random mutational processes acting on Junk DNA over a period of some 20 million years and both processes randomly produce the same high order result.

What are the chances of an undirected random process producing this result?
If anyone wishes to believe in miracles, then you are staring at one.

On page 509 Collins discusses this finding under the heading

Co-localization of SINEs in rat and mouse
Despite the different fates of SINE families, the number of SINEs inserted after speciation in each lineage is remarkably similar:,300,000 copies……Figure 9c displays the lineage-specific SINE densities on rat chromosome 10 and in the mouse orthologous blocks, showing a stronger correlation than any other feature. The cause of the unusual distribution patterns of SINEs, accumulating in gene-rich regions where other interspersed repeats are scarce, is apparently a conserved feature, independent of the primary sequence of the SINE and effective over regions smaller than isochores.

Notice how this reference to isochors is just glossed over. Why? Because Junk DNA is becoming an embarrassment It was used by Jerry Coyne amongst others as proof of Darwinian evolution. Now it is viewed as conserved, but lets not dwell too loudly on that.

When looking for functionality the first thing geneticists try to spot is a distinct non random pattern. This is what we have here and we all know what non random functional patterns reveal.

However since an outside agent cannot be considered we are left with random mutations being the miracle worker.
So am I being selective. Well we can examine the other graphs if anyone wishes.
btw the Human genome produces the same pattern.
The whole genome is an organised entity as is being clearly demonstrated, not the cobbling together of random undirected mutations.

[Gavin]

scottie, are you sure you're not a creationist? You seem to use their tactics a lot. Gee, science doesn't have a good answer for this. I guess god must have done it. When science has figured out everything, we'll get back to you. Until then, read the last paragraph of the section you quoted from.

[scottie]

Gavin
Sorry for the delay, on my travels away again.

I am disappointed that you are so reluctant to engage in the science underpinning your view.

are you sure you're not a creationist? You seem to use their tactics a lot. Gee, science doesn't have a good answer for this. I guess god must have done it.

Actually science reveals the right answer. The evidence from science is demonstrating that this view you are presenting cannot be supported by random and unguided natural processes.

If you are suggestion that I am using creationist tactics then they must be well pleased with your "compliment" because I have been presenting only the evidence that science itself reveals.

Your reference to the last paragraph which I have quite naturally read, states

These phenomena, in conjunction with an overall trend in substitution rates towards AT-richness, suggest a model in which quickly evolving regions accumulate a higher-than-average AT content, which attracts LINE elements. Although distinct cause– effect relationships such as this remain largely speculative, these results reinforce the idea that local genomic context strongly shapes local genomic features and rates of evolution.

Isn't this is the way science works.
One looks at the evidence, then formulates a hypothesis that can explain it, paying particular attention to stating clearly what the assumptions that underpin that hypothesis are based on.

Now when speculation is the best some of these scientists can come up with, you either run with that speculation or call it for what it is.
That is all I am doing.
I realize it is upsetting to you but I didn’t join this forum to run with the crowd or indeed be intimidated by it.

When science has figured out everything, we'll get back to you.

Who is the We ?

You seem to be confusions one noun "science" with another "scientists"
Is that not rather presumptuous?

[LeoPol]

Hi! Thus, the origin of life began with the origin of the mind. And then the mind, picked up the knowledge and created a polypeptide-nucleic technology! Armed with this technology and has spread throughout the universe.

(Comment 101 by LeoPolishchuk)
http://richarddawkins.net/articles/6435 ... egin#page4

"In order for a origin of membrane - much organic matter is not necessary - only the membrane lipids of different isoforms, it is necessary also to a weak emission core of the star created a flow of heat through the surface phase transition, and yet not interfere with a certain oscillation - vibration … In general, all this is difficult to discuss now, not yet studied the process of emergence and functioning in a natural cell membrane of this very … - Active situational model - a kind of natural intelligence and personality!! But when it all becomes clear, then we can speculate about the conditions and awakening him on the protostar, or on some planet out there."

[Gavin]

I am disappointed that you are so reluctant to engage in the science underpinning your view.

Experience has taught me that doing so is futile. Closed minds are difficult to reason with. The issue is neither the lack of evidence supporting evolution nor the wealth of evidence supporting supernatural creators, but why we all believe what we do.

The evidence from science is demonstrating that this view you are presenting cannot be supported by random and unguided natural processes.

Few natural processes are random, but they do appear to be guided - by natural laws.

Now when speculation is the best some of these scientists can come up with, you either run with that speculation or call it for what it is.
That is all I am doing.

In the absence of answers, speculation is all we can do. But speculation is the source of further research. You haven't convinced me that your belief in a supernatural creator is speculation on your part.

Who is the We ?

"We" are the forum members who understand how science works.

You seem to be confusions one noun "science" with another "scientists"
Is that not rather presumptuous?

No. I don't see any other group using a systematic, rational approach to looking for answers.

[scottie]

Gavin

scottie wrote:Who is the We ?

"We" are the forum members who understand how science works.

Would you mind terribly if I demonstrate how I understand science works and perhaps any forum members could then comment whether my understanding is correct.
Perhaps a good start could be by putting the case for phylogenitic trees that you introduced but the details of which you now don’t wish to discuss.
Below is a broad paraphrase description from wiki that I essentially agree with.

A phylogenetic tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics.
The taxa joined together in the tree are implied (or inferred) to have descended from a common ancestor.

The website talkorigins has a very good primer on this subject.. A lot of it is very technical but much of it is understandable even to a layman such as me.
http://www.talkorigins.org/faqs/comdesc/phylo.html

At the very end of this primer is the subheading

Caveats with Phylogenetic Inference
As with any investigational scientific method, certain conditions must hold in order for the results to be reliable. A common premise of all molecular phylogenetic methods is that genes are transmitted via vertical, lineal inheritance, i.e. from ancestor to descendant.
If this premise is violated, gene trees will never recapitulate an organismic phylogeny.

This assumption is violated in instances of horizontal transfer, e.g. in transformation of a bacterium by a DNA plasmid, or in retroviral insertion into a host's genome. During the early evolution of life, before the advent of multicellular organisms, horizontal transfer was likely very frequent (as it is today in the observed evolution of bacteria and other unicellular organisms). Thus, it is questionable whether molecular methods are applicable, even in principle, to resolving the phylogeny of the early evolution of life near the most recent common ancestor of all living organisms

(my emphasis)
It then goes on to list some of the some of the more important caveats. (about 11 in total)
This is all coming from an evolutionary site and is a very honest presentation of the evidence.

Please note the expression “phylogenetic Inference”.

Now it is very clear that the hypothesis of Horizontal Gene Transfer has considerably muddied the waters in establishing the tree of life and hence common ancestry
So as this site recognises, it was very common in prokaryotes and thus the last universal common ancestor cannot be determined through molecular means.
The base of the tree therefore cannot be distinguished in any diagram..

Since HGT is inferred to have played such a ubiquitous role in early evolution, I would suggest perhaps HGT also needs an explanation.
Can anyone please assist?

[JackBean]

scottie, are you sure you're not a creationist? You seem to use their tactics a lot.

agree, quote mining, avoiding unwanted topics etc.

[Gavin]

scottie

You're getting back to the crux of the matter by addressing the issue of scientific inference. In the absence of absolute truth, inference, through inductive and deductive reasoning, and based on the available evidence, is the best we can do. No phylogenetic tree, or anything else for that matter, is proven to be perfectly known. We can only collect data and propose probabilities based on those data. New data often force revisions. We will likely never be able to build a complete tree of life that will have any substantial probability of accuracy, and we will certainly never KNOW any tree to be accurate, especially for the early stages of life where things like HGT have muddied the waters. I don't know that evolution is true any more than you know that your creator exists. But the body of evidence collected to date favours evolution more than it favours creation - by a large margin. You may interpret the evidence to favour your beliefs all you want, but doing so will have little impact on the scientific world.

As I keep saying, you believe what you want to be true. The evidence points elsewhere.

[scottie]

Gavin
I agree with just about everything you have said except the last two sentences.
It is in the area where you state that the weight of evidence falls in favour of Darwinism that you are unable substantiate.
It is in just this area that I have been producing the weight of evidence and citing the peer reviewed support for it that you have been unable to contradict.

The only argument that you seem able to produce is by way of vague statements
like

But the body of evidence collected to date favours evolution more than it favours creation - by a large margin.

A statement like that should be backed up, not just made.
I am backing up my argument from actual evidence reported on by evolutionary scientists themselves.

However I do give you much credit for acknowledging that your stand is essentially a philosophical one, and one with which I have no problems because I take it to be a sincere one

However it is when you say it is backed by science then I respond that you really have to demonstrate that.
The weight of evidence that you keep referring to is evidence that supports variation within species.
I don't think even the so called "creationists" who believe that life somehow continues after death, disputes that fact.

I find it difficult why on a biological blog no one is prepared to, for instance, engage on the subject of HGT.

Why?
it's a perfectly valid biological subject, one that prompted a lot of detailed research.

You apart, I sense some trepidation to engage in anything that can be analysed scientifically.

So I ask again, is anyone prepared to at least engage on HGT as it impacts on the very subject you yourself introduced.

[Gavin]

You're becoming tiresome, scottie. If you really want to believe that science favours the existence of a creator over evolution, then go ahead. Your faith is stronger than your ability to reason and seems unshakeable, so any effort on my part to shake it appears to be futile. Science requires an open mind to be effective.

Don't be too offended if members of the forum don't take you seriously. We get many deniers here, and sometimes we just get tired of them, or annoyed with them. I'm not annoyed, but I am tired.

[scottie]

Gavin

Don't be too offended if members of the forum don't take you seriously. We get many deniers here, and sometimes we just get tired of them, or annoyed with them. I'm not annoyed, but I am tired.

Why on earth should I be offended. You have a view and I have a view.
However what is it that I deny?
Is it Science or your philosophy?
I am simply presenting the evidence of science and you are presenting the philosophy.

Now you surely cant deny that?

The views on this thread are increasing by over 1500 on average per day.
It seems many are quite far from getting bored, unless of course they enjoy being bored.

Gavin I don't except you to respond, but at least listen to what evolutionary scientists themselves are saying.
Not the ones who write books denying the evidence, but the ones who are actually doing the research and acknowledging the difficulties Darwin has created.
I am not simply an outsider denying Darwinism. My roots are firmly within science.
The denying is coming from within the evolutionary community itself.
You may not wan't to embrace my design view and I don't have a problem with that, but at least acknowledge the evidence against Darwinism.

As I see it, the problem you are faced with is that your materialist view (and I have due respect for that) has led you into accepting a dogma, one that insists Darwinism and Science are one and the same thing and anything that disagrees with it is not scientific.

Well the situation is, the evidence from scientific research is rapidly unraveling that dogma and I fully understand how difficult it must be to come to terms with it.

However the scientific method is what matters in the end, and adhering to that is what advances knowledge and understanding.

Perhaps if I press ahead with the case for HGT as presented by the evolutionary community maybe I and perhaps others can learn some more.