Theories - Origin of Life

[LeoPol]

Oh, thank you, this is interesting! But our situation is better! Our version of the ID do not want creationism.

[scottie]

Jackbean

Sorry for delay in responding. I have been away for a few days.

JackBean » Mon Sep 05, 2011 8:55 am
Can you tell, how exactly the metabolic processes are against the natural laws? Because I'm pretty sure they are not.

I think you misunderstand what I am saying.
Let me try and clarify.

The molecules involved in metabolic processes, without a guiding outside source of energy will follow the natural laws and disintegrate down to their elemental natural states.

I have approached this subject before but I feel it is now important to revisit it again.

Lets take the question as to what happens at death?
In other words what is the difference between, say, a living dog and a dead one?

At the moment of death, all the processes we have studied in biology cease and the dog begins to disintegrate.
However that disintegrating corpse is still subject to the same laws of physics and chemistry as the live dog was, so what was keeping the live dog living?

At the moment of death all the biochemical molecules in body are the same as when it was alive. The same functional information in the molecules remains, yet function has ceased.

Now ask yourself what kind of logic are we appealing to which suggests, that by assembling all the molecules together (assuming we are able to of course) into the form of a dog, we will create a dog that lives, or indeed any form of living organism.

Doesn’t all our experience, data and intuitive understanding tell us that life is something apart from mere chemical molecules?

Life is what keeps the chemical molecules that make up our bodies from following the natural laws that send these molecules back to their constituent parts. When life is removed these molecules begin reverting back to what they were originally.

I hope that explains my point more clearly.

btw I am not arguing for the ID community. There are some fundamental difficulties I have with their line of argumentation.
I will be happy to explain in more detail if called upon.


Leopol

Sorry but I am having great difficulty in understanding your posts.
It maybe a language problem.

[TheMatrixDNA]

Hey guys,

I'm writing a paper on the origin of life, and I need some suggestions about which theories to write about. Obviously there are tons of them, so any suggestions, information, or references you guys can give me would be great.

Hi, Chilipanda,

What about a theory that suggests there were no origins of life in this natural Universe because it connects Cosmological Evolution to Biological Evolution? This theory is the result of comparative anatomy between the first cell system and the last non-living system, which built a model of LUCA (the last Universal Common Ancestor), a kind of building blocks of astronomic systems, the lost link between the state the world about 4 billion years ago and the first nucleotide at Earth. The theory suggests the DNA as a universal template, called The Matrix/DNA. So, it is not panspermia, only suggesting that there was a hidden variable ( the matrix ) at the primordial soup.

Ok, I am the author of this theory which has cost to me about 30 years of hard work. As an agnostic I don’t believe in this theory but the amount of evidences and right predictions are becoming astonishing and I am testing the models. I need ideas for testing/discussing and your topic – as I am following it – is very interesting and helpful. I should be grateful if you permit to participate in this debate. At least, I can suggest faults and gaps on the existents theories that nobody else has thought about. I can do it? Cheers…

[TheMatrixDNA]

Everyone that has ever commented on the origins of life are reduced to their opinions, even the great Richard Dawkins is left to speculation.

Hi, Believer,

There is a set of natural laws and mechanisms. If you know them and follow biological evolution in the reverse way towards biological systems origins, you will be no “left to speculations”.

Feel free for asking or pointing out when you think there are gaps.

But, then, you will arrive at the state of the world before life’s origins, the world that created life. If you apply the same set of laws for calculating that state of the world you will get a surprising cosmological model, where Astros exists under life’s cycles and performing perfect closed systems. The blueprint of this model is a building block, identical to a nucleotide, the fundamental unit of information in the DNA. So, there was no origin of life at Earth, because Earth, itself, belongs to a system that is half-living.

So, the right calculations using only natural laws and mechanisms you discovered that there is a link between biological evolution and the past cosmological evolution: the DNA template.

Continuing going deep to the past, with those laws, you will arrive to the primordial nebula of atoms systems. But, then, you will have a more complex model of atoms: they have the principles of life’s properties.
Go deepest, before the atom nebulae, and you will meet with empty vortexes. But, you will see that those vortexes have the laws, the mechanisms and all life’s properties.

Now you are going to before the Big Bang, leaving this Universe and believing that those vortexes are bits-information, like genes, coming from a natural system, ex-machine. That could be your God. To me, it means merely more research work to do…

[scottie]

As promised in a previous post, a transcript of an interesting conversation

This year's Annual Edge Event took place at Eastover Farm in Bethlehem, CT on
Monday, August 27th. Invited to address the topic "Life: What a Concept!" were
Freeman Dyson, J. Craig Venter, George Church, Robert Shapiro, Dimitar Sasselov, and Seth Lloyd, who focused on their new, and in more than a few cases, startling research, and/or ideas in the biological sciences.

http://www.edge.org/documents/life/Life.pdf

You will find more information on the scientists including video clips from this event.
http://www.edge.org/documents/life/life_index.html
The video clip of Robert Shapiro is quite interesting.

I would recommend spending some time reading and viewing this.

Here is part of the transcript of the Event.
Discussion between Venter, Church and Shapiro.

Page 76

CHURCH: I'm a little more interested in the future than the past — but I don't
dismiss it either. For example, on the top of Freeman's wish list was ribosome
archaeology. And Dimitar asked, Is there a milestone that we think is significant.
The ribosome, both looking at the past and at the future, is a very significant
structure — it's the most complicated thing that is present in all organisms. Craig does comparative genomics, and you find that almost the only thing that's in common across all organisms is the ribosome. And it's recognizable; it's highly conserved. So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be?
The only way we're going to become good scientists and prove that it could come into being spontaneously is to develop a much better in vitro system where you can make smaller versions of the ribosome that still work, and make all kinds of variations on it to do really useful things but that are really wildly different, and so forth, and get real familiarity with this really complicated machine. Because it does a really great thing: it does this mutual information trick, but not from changing something kind of trivial, from DNA to RNA; that's really easy. It can change from DNA three nucleotides into one amino acid. That's really marvelous. We need to understand that better.

VENTER: And you can't have life without it.

CHURCH: Definitely. It's common to all life. We need to understand that, and the way we're going to fund it — there's not that much funding for prebiotic science, but if there's a lot of funding for understanding the ribosome in the future and in the present, inevitably it will much enable studies of it in the archaeological and ancient biology sense.

VENTER: But using these tools, it's my hope we can do something similar to what you suggest. We can extrapolate back once we have the database of Planet Earth genes to what might have been a precursor species, and then we should be able to build that in the lab and see if it was really viable, and then start to do component mixtures to see if you can spontaneously generate such things.

CHURCH: But isn't it the case that, if we take all the life forms we have so far, isn't the minimum for the ribosome about 53 proteins and 3 polynucleotides? And hasn't that kind of already reached a plateau where adding more genomes doesn't reduce that number of proteins?

VENTER: Below ribosomes, yes: you certainly can't get below that. But you have to have self-replication.

CHURCH: But that's what we need to do — otherwise they'll call it irreducible complexity. If you say you can't get below a ribosome, we're in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins.

VENTER: In the RNA world, you didn't need ribosomes.

CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins.

VENTER: Yes.

SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously.

CHURCH: It won't form spontaneously; we'll do it bit by bit.

SHAPIRO: Both are obviously products of long evolution of preexisting life through the process of trial and error.

CHURCH: But none of us has recreated that any.

SHAPIRO: There must have been much more primitive ways of putting together catalysts.

CHURCH: But prove it.

Notice how both Church and Venter agree that the ribosome has no precursor, in fact Church recommends that the ribosome is the candidate for the ID community to concentrate on as an example of irreducible complexity.

So the evidence is quite clear to these scientists, but note Shapiro’s interjection

Both are obviously products of long evolution of preexisting life through the process of trial and error.

Here you have an obvious example of a renowned scientist whose thinking is guided by his philosophical view rather than by evidence.

[LeoPol]

scottie
I decided to speak out on three topic at Dawkins. But controversy still slightly opened only on one: http://richarddawkins.net/discussions/6 ... ure?page=1 .
The other two - Brake.
( - http://richarddawkins.net/discussions/5 ... FrIJIB6U8g
- http://richarddawkins.net/discussions/6 ... ife?page=4 )
Is there a bad translation and turned out? I tried so hard!

[scottie]

Leopol

There clearly is a problem in translating from Russian and it does make understanding your posts a little difficult. However you must be commended for trying.

I have spent some time in trying to understand your position, so let me try and respond to your view.

As I am beginning to understand it, you use the expression

Nucleic-acid-peptide micro-molecular technology

In other words it seems to me that you appear believe that a technology has been developed in the past whereby peptide chains could be produced, thereby providing the ability to make cellular life.
This technology has been transferred to the earth and that accounts for our present condition.

I think you agree that this view is highly speculative, but more than that I believe you are making the same basic mistake that evolutionary theory an indeed ID theory make, that is, the appearance of life has been through a bottom up process.

In other words you start with basic building blocks ( pre-biotic and then biotic) and then build up the whole organism, this essentially summarises the evolutionary view.
The ID view ( as I understand it) has a similar perspective in that the designer has built up the organism in a Lego-like assembly way.

However this does not reflect what we observe in reality.
Let me try and explain with an example.

We tend to see the cytoskeleton portrayed as a fixed structure,
But that is simply incorrect

“ … it is not a fixed structure whose function can be understood in isolation. Rather it is a dynamic and adaptive structure whose component polymers and regulatory proteins are in constant flux.”

Cell Mechanics and the Cytoskeleton – Nature 463 Jan 28 2010 485-492)

The cell is typically about 80% water and when examined we note that the main activity is a pattern of flows. What we see are fixed structures that actually are part of these flows.

Craig Holdrege in his book “ The dynamic Heart and Circulation” describes the development of the heart this way
http://www.natureinstitute.org/pub/ic/ic7/heart.htm

We see that blood flow, the form of the heart, the pattern of its fibers, and the motion of the heartbeat are intimately entwined. We can't think of one without the others. When we go back to the origin of the blood and the heart in embryonic development, it is no simple matter to say what came first. Early in its development the heart begins to form loops that redirect blood flow. But before the heart has developed walls (septa) separating the four chambers from each other, the blood already flows in two distinct "currents" through the heart. The blood flowing through the right and left sides of the heart do not mix, but stream and loop past each other, just as two currents in a body of water. In the "still water zone" between the two currents, the septum dividing the two chambers forms [1]. Thus the movement of the blood shapes the heart, just as the looping heart redirects the flow of blood.

We have been educated to see the living organism as an assembly of individual parts,for example like a watch that is put together in a certain way.

However in a living organism, (as one writer puts it)

the parts grow within an integral unity from the very start. They do not add themselves together to form a whole, but rather differentiate themselves out of a prior wholeness… They are growing even as they begin functioning, and their functioning is a contribution to their growing. The parts never were and never are separate, never assembled.

Both the evolutionary and ID views have this common foundation. They have a bottom up perspective of living organisms, when in fact the reverse is the case.
It is the whole that determines the parts. This whole is determined from the moment the two gamete cells join to form the Zygote.

It is this wholeness that scientists have not been able to come to terms with, and the result has been a fruitless search for some understanding as to how these parts could have come together to form the whole we see and indeed are.

Chemical molecules do not come together to form life.
Even cutting edge biologists such a Craig Venter and George Church are beginning to recognise this fact.
(The little transcript of their conversation at the Edge event that I had in my last post reveals this)
They are only one step removed from recognising that life uses chemical molecules to persist. When life ends these molecules revert back to their constituent parts.

We know of no instance where life has come from any source other than another life.
To try and show that it can and indeed has is no different than looking for fairies at the bottom of some garden.

[JackBean]

No, Venter says, that the precursor is from RNA world, but since we don't have no such ribosomes nowadays (w/o proteins), we cannot reduce the number of proteins to less than 53.

[JackBean]

Lets take the question as to what happens at death?
In other words what is the difference between, say, a living dog and a dead one?

Ahh, you mean this...
The molecules are still the same, they are just not regulated. Even the cells do not die immediately after death, but they survive a little, although they are not synchronized anymore and of course, the shortage of supply causes their death later. This was discussed in another topic recently.

btw I am not arguing for the ID community. There are some fundamental difficulties I have with their line of argumentation.
I will be happy to explain in more detail if called upon.

Please, go on.

[LeoPol]

scottie
Thank you!
The hypothesis is that the cell membrane - this is a direct descendant of the brilliant engineers who have several billion years ago created "Nucleic-acid-peptide micro-molecular technology". That's membrane and is the carrier of "consciousness" - what we call 'I'. Everything else - equipment.
You can say so, that in every cell membrane formed a kind of cellular "self", which is the "active model of the world in an electromagnetic field of the membrane."

I must add that this hypothesis is very useful in molecular biology, because it creates a theoretical model of cell entity which manages all the cellular technologies. A lot gets new meaning clear! At least, now we need to look for those instructions that guided this subject!

[scottie]

Jackbean

Thanks for your response.
May I deal with your points in turn for fear my post will get too long, something for which in the past I plead guilty.

No, Venter says, that the precursor is from RNA world, but since we don't have no such ribosomes nowadays (w/o proteins), we cannot reduce the number of proteins to less than 53.

Firstly please note what he previously said about the ribosome

And you can't have life without it.

Also what Venter actually then said was this

In the RNA world, you didn't need ribosomes.

The RNA world is a speculative scenario that many are clinging to in order to have some hope of progress. However even Venter knows that is a speculative hope. He probably was not aware at that time of the NASA report (I have referred to it previously) which stated quite clearly that there are no plausible hypothesis for routes to complex biochemical molecules, either chemically or thermodynamically.

So probably not even being aware of the NASA conclusion at that time he remained in the speculative world of RNA

Now if you wish to remain there as well, then that's OK it's your choice, but please, remember that science is not backing you up.

Now on the question of organism death you responded

Ahh, you mean this...
The molecules are still the same, they are just not regulated. Even the cells do not die immediately after death, but they survive a little, although they are not synchronized anymore and of course, the shortage of supply causes their death later. This was discussed in another topic recently.

You are right we have discussed this before, and forgive me when I state that I feel you may not have quite grasped the point I was making.

At the moment just prior to death all the biochemical molecules in the dog are still functioning and intact.
At the very moment of death they are still there, however as you rightly point out the regulatory mechanisms cease and the molecules begin to disintegrate.

In other words, the natural laws of physics, chemistry and thermodynamics continue operating but without the guiding regulation that has now been removed, and the result is degeneration, down to their constituent parts.

Therefore the natural course that natural laws take, breakdown biochemical molecules.
Since that is the case how can those same laws naturally guide the building of cellular life let alone the whole organisms
They have to be guided down the different regulated pathways if they are to succeed.
So whatever life is, it is certainly not a constituent part of physics or chemistry.

That is why a naturalist view of the origin of life is scientifically untenable.

That is also why NASA has been forced to draw the conclusion it has.

If any organisation needed a natural explanation to life’s origin it is they.Just think of all the funding they would receive if they could. There is every incentive for them to prove that they have conquered the problem of Abiogenesis, and if they were able to then I will let you speculate on the news headlines!!

One further point to note.
Nobody has been able to describe what life actually is.
There are many who have tried to define it in one way or another, but there is no consensus even on this basic point.

One rather cute tribal description is :-
“Anything that is capable of Darwinian evolution”.


I will deal with the ID situation very shortly in the next post.

[scottie]

Here are problems I have with Intelligent Design theorists.
This is what they have to say.
http://www.intelligentdesign.org/faq.php

Is intelligent design theory incompatible with evolution?
It depends on what one means by the word "evolution." If one simply means "change over time," or even that living things are related by common ancestry, then there is no inherent conflict between evolutionary theory and intelligent design theory. However, the dominant theory of evolution today is neo-Darwinism, which contends that evolution is driven by natural selection acting on random mutations, an unpredictable and purposeless process that "has no discernable direction or goal, including survival of a species." (NABT Statement on Teaching Evolution). It is this specific claim made by neo-Darwinism that intelligent design theory directly challenges.

There appears to be a contradiction in the above statement.

A fundamental doctrine of Darwinism is the principle of common decent/ancestry, and yet some adherents of ID ( Michael Behe for example) endorses this principle of common ancestry.

If there is common ancestry then there has to be a mechanism that engenders this process. I have not seen that explained anywhere. Darwin explained his mechanism.

Also, by way of an example, why would a designer tie a human being to an ape through common ancestry.?
Why not make each separately?

It seems to me that some of the ID community are facing both ways. I have tried to find an explanation as to how this is not a contradiction but have been unable to as yet. Maybe some one will be able to enlighten me.

However there is a more fundamental problem in which ID is explained.
Perhaps I could illustrate it this way.

If I am to design a house, I don’t start with designing certain aspects of it say, the kitchen sink, then the bathroom mirror or bedrooms etc and then try and fit them all together to provide an overall framework.
In other words I don’t start from the bottom and work upwards.
This is how evolutionary theory is explained. (i.e. a bottom up approach)

Design however implies purpose. Therefore it is a top down action.
So, to try and explain design as ID proponents do in finding structures within an organism that are, for example irreducibly complex and then stating that this is evidence of Intelligent design is not sufficient.
A living organism is more than the sum of all it parts.

Also they appear to present a mechanistic view of organisms, a sort of sum total of biological machines.
The very icon of the ID community is presented as an outboard motor. (the bacterial flagellum).

When something is designed, there is always a purpose to the design.
The various parts that go into that design always grow out of that purpose.

Now I don’t see the ID community addressing this anywhere in their literature. In fact they appear to concentrate on simply refuting neo Darwinism.

Actually there is nothing wrong in presenting evidence that corrects a wrong idea.
I myself can be successfully accused of that.
Certainly the work they do is very informative and I have learned a lot from them as indeed I have from the evolutionary community.

However there is no apparent attempt to replace that idea (neo Darwinism) with another that demonstrates purpose.

They are shying away from the obvious implications of what design means.