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Consideringlily, Oncedeceived and defining evolution

Oncedeceived

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Why not? I mean, sure, the chances of a human chromosome forming spontaneously is next to impossible, but we're not talking about direct formation of a specific chemical, but the proposed formation of a class of chemical. Nucleic Acids for instance.

Nucleic acids alone would not bring forth any formation of life on its own...even a more simple life form as we know it. IF the life form was different we would then need to ask how this life form would be sooo different from every other life form on the planet. Every life form on this planet is cellular. Every life form. It seems to me at least, that for an ancestral life form to be something that has no connection with the complexity of the single cell, would be unlikely. You would also have to get around the problem of the proteins being necessary as well.


It is no red herring. Unless you can show that there is a simplier molecule that can be a pre-cursor to life then it is just a just-so story without any evidence to back it up. Just- so stories are not evidence and the arguments against it are in no way red herrings. You have no way to falsify your argument and it can not be tested scientifically.


hmmmm...Now you are asking me to get into specifics. There are thousands of control mechanisms in the average cell...but getting me to name and describe a single one is a pain.
You can not jump to the cell for the mechanisms since you are claiming that this mechanism is before the cell originated.

This explanation is certainly a mechanism but it is a mechanism of an already formed cell. You have not given rise to the cell in your theory. You must show mechanisms in a non-living molecule.

But you can discuss the origin of life without confusing it with the complexity of evolved life. Don't strawman this argument by trying to force the origin of life to deal with modern cellular constructs. They just are not relevent.
Oh but they are, and you are trying to divert origins from the outcome. Regardless of what life form first arose, there is no evidence of it. Constructing possibilties without evidence does not provide valid information. For any early life form it must be shown (be in evidence) that life as we know it could arise. It is relevant, in fact, necessary to the cellular constructs that are present in all life forms on earth.



My contention is that life is cellular. Many things can be said of life but this one thing is the common ground of all living things.
The point here is, YOU have to deal with the fact that you discern between life and non-life, while for me the fact that all 'life' is made up from non-life, is just obvious. There is nothing BUT non-life.
This to me seems like a cop out. You can't show any evidence for your hypothesis, so your theory is not sound in scientific terms.



The irony of the fact that you are using the word of thousands of scientists, all of who believe that life started from non-life, to support your argument is lost on you isn't it?
Not at all. I have no problem with scientists nor science. The scientists are under the requirment of their philosopy. Regardless, the scientists that believe life started from non-life are still unable to show that. Their theory so far is not in evidence.

I'm sorry, what? I don't know what you mean.
 
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A

Aegist

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Oh dear. You seem to bring about a confusion of everything which is said. I reply to something in context, then you reply to it from a completely different angle... For instance you said:

in response to what I said:
Aegist said:
Why not? I mean, sure, the chances of a human chromosome forming spontaneously is next to impossible, but we're not talking about direct formation of a specific chemical, but the proposed formation of a class of chemical. Nucleic Acids for instance.
which was clearly in response to:

Oncedeceived said:
Compounds do form given the correct conditions to do so. Simple compounds do form, but the complex molecules needed for life are not so simple and do not spontaneously form.

Please PLEASE respond in context, or else establish why you are taking my comments out of context.

Your first comment agreed that molecules formed, but that complex ones (such as those found in living organisms (ie: DNA, Proteins lipids) can't form. I counter-claimed that point by asserting that concatomers can form and make the complex molecules found in life (such as DNA), to which you reply that DNA won't make life.

THAT is where you jumped topic. this point was NEVER about LIFE, it was about the formation of complex chemicals. You either agree that complex molecules can form spontaneously or you don't. You can't refute my point about complex molecule formation on the basis that it isn't life. I never said it was life!

If we are going to discuss something, I am going to need you to try harder to respond to the line of conversation that is occuring, without jumping topics and points. Else this is not a conversation.


It is no red herring. Unless you can show that there is a simplier molecule that can be a pre-cursor to life then it is just a just-so story without any evidence to back it up.
This is partly a consequence of your confusion above. It WAS a red herring until you made it be about spontaneous formation of 'THE LIFE COMPLEX MOLECULE', which it never was.

And like it or not, we are discussing something here which hasn't been proven yet. To consistently revert to "Until you prove it, you are just making it up" is pointless. If you want to take that stance, then lets stop talking now. You know as well as I do that we don't have THE answer for this, it is all speculation, but it is speculation which has been guided by science, investigation, experience with modern life and understanding of chemistry.

For instance:
Aegist said:
Self-Reproducing Molecules Reported by MIT Researchers
http://w3.mit.edu/newsoffice/tt/1990/may09/23124.html

is indeed evidence of a simple molecule which can self replicate...a pre-cursor of life perhaps? Almost certainly not THE pre-cursor of OUR LIFE, but perhaps A precuror to A life? If we can do it in the lab, then there is a good chance that such a thing can happen in a billion years somewhere in the globe.

Once again, not proof of anything, but its all about exploration of the problem, evidence, statistics, and discovering what is and isn't possible.

At the moment there is very little direct laboratoy evidence of life forming from non-life, but it is common concensus that life did still form that way, simply because there is no other alternative which is nearly as parsimonious as that hypothesis.

And here again we have the same jumping of topics confusion that I showed you above.

I described life as nothing more than non-life which acts with sophistication. That is what I defined life as (in this particular line of conversation), and you asked exactly what that meant, how does non-life interact with sophiostication, and I gave you a list: regularity, feedback, control etc, to which you asked for an example, so I gave you an example. Of course my example came from a living organism, because that is what we were talking about!!!! That is what the entire point was! Life, LIVING STUFF, is nothing but non-living stuff interacting with a higher degree of sophistication. These feedback mechanisms etc are ONLY (nothing else) non-living chemical interactions. Every life function going on inside you and every other life form can be described in non-living chemical detail, and every part of it can likely be recreated outside of living cells.

So anyway, I did not claim that this mechanism was before the cell originated, but the chemistry behind these control mechanisms certainly was. And most importantly, all of the mechanisms in a living call can be done outside of the living cell (take PCR for example). So my point remains.


But no they aren't. That is like arguing that skin has always been around because animals can't live without it, therefore any precursor to humans MUST account for skin. It must either have skin or it must have a precursor skin. Yet cleary it just isn't true because thanks to evolution, things have changed far more than we could imagine by ourselves. FAR more. And as of the origin of life, life started evolving. Everything could have changed. Everything. Who knows if the origin of life wasn't like Richard Dawkins postulated in the Blind Watchmaker: a sort of clay duplication of crystal structures...and then these clay structures actually bonded to molecules and made a performed as a sort of template to catalyse the creation of completely different chemical molecules?

Just because DNA replicates itself exactly doesn't mean life ALWAYS was DNA replicating itself. Clearly we can see that DNA can produce proteins, and only recently have we started seeing Prions emerge. What if in the next hundred years DNA mutated and started creating a protein which made a SUPER PRION. And this prion replicated itself with such fervor and such wonton destruction that is actually took over ALL organic molecules on earth? We would find ourselves with a planet under the cover of a Protein based genetic system with evolving organisms competing for replication rights.

DNA can lead to Protein replication. Maybe clay can lead to some molecular replication which can lead to DNA replication. And maybe none of those require lipid bilayers for it to happen! The current makup of "Cellular Life" is not important, because we are looking at a past which has evolved drastically from the origin.


My contention is that life is cellular. Many things can be said of life but this one thing is the common ground of all living things.
Viruses. Non-cellular, replicating

This to me seems like a cop out. You can't show any evidence for your hypothesis, so your theory is not sound in scientific terms.
Life is a definition. You show me an undisputable way of defining life, and then I will agree that we need a 'scientific hypothesis' to prove it exists.

The fact is Life is a human definition, and that has nothing to do with 'hypothesis'..it has to do with choice.

There were many things we haven't been able to show...LOL. God of the Gaps gets smaller every day

I'm sorry, what? I don't know what you mean.
Then lets leave this alone then.
 
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Oncedeceived

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Oh dear. You seem to bring about a confusion of everything which is said. I reply to something in context, then you reply to it from a completely different angle... For instance you said:

I agree that this conversation has drifted and is somewhat confusing.



Please PLEASE respond in context, or else establish why you are taking my comments out of context.
I don't agree that I have taken anything out of context.

Where did I say that DNA won't make life?
The whole excersise of this thread is about life.
If we are going to discuss something, I am going to need you to try harder to respond to the line of conversation that is occuring, without jumping topics and points. Else this is not a conversation.
I think I am beginning to see that.


This is partly a consequence of your confusion above. It WAS a red herring until you made it be about spontaneous formation of 'THE LIFE COMPLEX MOLECULE', which it never was.
Excuse me? We are discussing, or at least that is what this conversation began to be, the break down of knowledge and support for the cladogram.

The scientific evidence is not present in regards to the foundation or root of the symbolic tree.
Exactly. My point was that it was not in evidence. What we do have in evidence does not provide the necessary requirements of the scientific model. Which is the whole point.

Speculation is the road to understanding, and while I do not discount it in anyway, it is only as good as the support behind it as you say. For the foundation of the cladogram we do not have a true reflection of its root, or at least a scientific answer for it.



We are talking about a pre-cursor for life and not "our life".

Good chances are good investigatory tools but nothing more without the finished accessment.


Exactly. So in real terms, there is little direct evidence but it can't be anything but life from nonlife so it has to be that way (in a naturalistic materialistic worldview). So in conclusion, we have what I said we had from the beginning. A break down of knowledge that the entire cladogram is based upon. The foundation is not in evidence.



This is not in evidence, as you have said.


Who says it can't does not make it so. Regardless of explanations, it has to be in evidence and it is not. Which is the whole excersise of this conversation; so I must assume that you agree with me. Correct?
A just so story only.
Considering the common make-up of life the ancestory relationship would most likely would have to be less drastic in regards to its make up.


Viruses. Non-cellular, replicating
It depends on who you are talking to whether or not viruses are considered living organisms.

What Is a Virus?
  • Viruses- nonliving particles
  • Viruses are one-half to one-hundredth the size of the smallest bacterium
  • Viruses are considered to be nonliving because they are not cells and do not exhibit all the criteria of life: use energy, grow, or develop, ...can replicates with a host
  • Host cell- a cell in which a virus replicates
  • Viruses are named after the disease they cause or the organ or tissue they affect
  • Example: adenovirus in adenoid tissue
  • Viruses given a genus name ending in virus, then a species name
  • Virsues that affect the same host are given a code number (T1 -T7 viruses for e. coli)
  • Bacteriophage- a virus that infects a bacterium
Viral structure
  • Inner core of nucleic acid, RNA or DNA
  • Capsid- outer, protein coat
  • Envelope found on larger viruses, surrounds capsid and made of similar material as plasma membrane of cells
  • Arrangement of proteins in the capsid determines virus shape and plays role in type of cell it can infect
Attachment to a host cell
  • To replicate, a virus must enter a host cell
  • A virus recognizes and attaches to host cell at a receptor site on host plasma membrane
  • Process is similar to puzzle pieces
Attachment is a specific process
  • Each virus has specific shaped attachment protein
  • Viruses are species specific: phages and bacteria, TMV and tobacco plants
  • Some are also cell-type specific: polio virus and human intestinal & nerve cells
  • Specificity helps for control of viruses; smallpox eradication in 1980
  • Harder to control non-species specific viruses like flu
Viral Replication Cycles
  • After attachment, virus enters host cell and takes over its metabolism
  • Viruses use two means to enter host:
    1. Virus injects nucleic acid like a syringe leaving capsid on outside of cell
    2. Enveloped virus attaches and is taken in by membrane of host to form a vacuole, which erupts later to release its nucleic acid
Lytic cycle
  • Viral genes, once inside host cell, take over host cell's genetic material
  • Host cell uses its own resources to make viral genes and viral proteins to assemble complete viruses
  • New viruses burst from host cell, killing it
Lysogenic cycle
  • A replication cycle in which viral nucleic acid is integrated into host chromosome
  • Begins with attachment and entry of viral genes into host cell
  • Viral DNA does not take over cell immediately
  • Provirus- viral DNA is integrated into host cell's chromosome
  • Provirus may not affect functioning of host cell and it may continue metabolic activity
  • When host cell divides, provirus is passed to daughter cells, this can continue for many years
  • Once activated, provirus will enter a lytic cycle where viral parts are made and assembled, they then burst out, killing the cell
  • Disease symptoms of proviruses
  • Herpes symplex I, Herpes symplex II and Hepatitis B are all lysogenic: dormancy with occassional symptoms
  • Chicken pox may have proviruses that remain dormant in nerve cells to become lytic later in life to cause shingles (infection of nerve cells)
Release of viruses
  • New Viruses are released two ways:
    1. Lysis- the bursting of a cell
    2. Exocytosis- active transport process by which materials are expelled or secreted from a cell
    Retroviruses
  • Many viruses contain RNA instead of DNA (example: HIV)
  • Retrovirus- RNA virus with most complex replication cycle
  • Reverse transcriptase- viral enzyme that produces double-stranded DNA from viral RNA
  • DNA copy is then inserted into host cell's chromosome and becomes provirus
  • Presence of reverse transcriptase is evidence for infection by a retrovirus
HIV: An infection of white blood cells
  • HIV infects white blood cells, new viruses leave by exosytosis to infect other white blood cells
  • Cells continue to function normally, so host may appear to be healthy but can pass virus on
  • Eventually, proviruses become lytic, destroying cells and reducing immunity to infection and disease
Viruses and Cancer

  • Tumor viruses are viruses that cause tumors
  • Retroviruses, papilloma virus (DNA virus causing warts), hepatitis B (DNA virus causing liver cancer)
Plant Viruses

  • First virus identified was tobacco mosaic virus
  • Not all plant viruses are harmful, tulips and other flowers enhanced by mosaic viruses
Origin of Viruses

  • Viruses are thought to be nucleic acids that break free from host cells while maintaining an ability to replicate parasitically within the host cells.
LINK: http://www.northstar.k12.ak.us/schools/wvh/science/dcox/Chapter%20outlines/bioch18.htm


Life is a definition. You show me an undisputable way of defining life, and then I will agree that we need a 'scientific hypothesis' to prove it exists.
All life is cellular.

The fact is Life is a human definition, and that has nothing to do with 'hypothesis'..it has to do with choice.
Perhaps. Choice has to do with more than you know.
There were many things we haven't been able to show...LOL. God of the Gaps gets smaller every day
He may have the last laugh.
 
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Tomk80

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Again my apologies for taking such a long time to respond.

In what way?
Reading back, I think I meant in the way that there was no real good discussion going on. It seemed more like throwing about accusations. But I don't really remember anymore.

If you agree with consideringlily perhaps you can provide the information that she didn't provide?
No, because what you were asking was that we provide (for example) microfossils of molecular structures. That cannot be done. What consideringlily provided was evidence that we find microfossils. By looking at these and what these microfossils produced (for example the stromatolites), we can gain insight in what microbiotic life looked like in the time shortly after it appeared. This can inform us about which kind of life forms stand closest to the base of the tree of life. From that we can gain insight in what the earliest life-forms looked like, which informs cladistics in the formation of cladograms.

But look at what you are saying. You first say that you do not claim that the ToE breaks down. But right in the next sentence, you claim that it is not a probable explanation for a certain phenomenon. How is that different from claiming the ToE breaks down at that point?

True, but when breaking this down there are numerous events that must occur for this to even be possible and those things...such as an explanation of how meiosis appeared.
I agree.

It also does not account for the appearance of the nucleolus. The Golgi apparatus needs to be explained.
I again agree.

This is a good link to show this:
http://www.beyondbooks.com/lif71/4e.asp
[FONT=Geneva,Arial,Helvetica,helv,sans-serif][/FONT]
To be honest, I'm not sure what you were trying to achieve with that link. Yes, the golgi apparatus has an important function and leaves behind a lot of trash. It's interplay with other functions is complicated and intricate, but so are many other things which are explained by evolution. The link did not contain any information on theories of it's evolution and what their pros and cons are.

Nor does it account for the microtubules which distinguish the eukaryotic cell. Above all, it does not explain how DNA came to be organised into chromosomes and enveloped in a nuclear membrane.
I also agree.

But realize that what you are talking about above is not in essence something that needs to be explained by the cladogram. In a cladogram, evolutionary relationships are portrayed. Or maybe more accurate, morphological and genetic relationships. Precise mechanisms are not offered by a cladogram.

The question then becomes whether the breakdown of the twin-nested hierarchy at the level of single-celled organisms, is really surprising when looking at the mechanisms observed in nature. But if we look at nature we see tha lateral gene transfer between single-celled organisms is common. As explanations go, the endosymbiont theory defenitely provides a good explanation for a number of organelles, such as mitochondria and chloroplasts. So that cross-over is seen between classes of single-celled organisms in the cladogram and that this makes ancestry in these classes hard to trace should not be a surprise. Given what we know about gene transfer in single-celled organisms, this is to be expected. So that in itself does not negate either common ancestry or the theory of evolution. I would argue that the universality of the genetic code argues very much in favor of such a common ancestry in the past.

I think the explanations are not so good when broken down.
In other words, you do think the theory of evolution breaks down at the bottom of the evolutionary tree. The theory of evolution proposes a purely naturalistic explanation for the diversity of life for all species. It is this that you seem to have problems with.

I agree that a lot of gaps remain with regards to the evolution of specific structures. I would argue that this is not only the case with molecular structures but also with many macro-structures and relationships in nature.

But what you are doing here is proposing to substitute "we don't know" with the word "God". I fail to see how substituting a word is in any way a solution to the problem. I would argue that it is worse than just an exercise in futility, as it implies certainty where there is none. How do you propose to distinguish between "I don't know" and "God". Only if you find a way to do that does such a substitution make sense.

I also fail to see how evolution is put out there like a God.
 
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Oncedeceived

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Again my apologies for taking such a long time to respond.

My apologies as well. We have problems with the internet when ice gets on the antenea.

Reading back, I think I meant in the way that there was no real good discussion going on. It seemed more like throwing about accusations. But I don't really remember anymore.

I can understand that.

I was talking about the statement that you agreed with Lily. In this instance (above) I totally agree. Unfortunately, knowing the earliest life forms and knowing their origin are two very different things.


Let me explain. Whether the ToE breaks down is only important in how you define it.

"In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next." - Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974


The theory of evolution has taken on many more facets that I think it can explain. Does that mean the ToE breaks down? It all depends on what you are claiming ToE is and does. The theory of evolution is man's interpretation of how living organisms were created. Sometimes it takes on a life of its own. We look at ToE and consider it the moving force in life rather than mechanisms and processes we find.






Good. Common ground.


I again agree.

Good again.


I was giving an example of an event that I felt showed the complexity of the unanswered questions of Margulis's thoery.



Very true. That being said though, the cladogram protrays the root in such a way, that protrayal is not in evidence. So the cladogram has a breakdown in the scientific evidence to support it.

Mitochondria are monophyletic. With the endosymbiont theory we would be lead to believe that they would be of polyphyletic orgin. This brings up a question as to the event itself.

The universality of the genetic code does not necessarily mean common ancestry as defined in ToE exclusively.


The ToE is a naturalistic explanation so I have no problem with that. It is when it breaks down or does not have naturalistic explanations that I have a problem with.
I agree that a lot of gaps remain with regards to the evolution of specific structures. I would argue that this is not only the case with molecular structures but also with many macro-structures and relationships in nature.

Yes.

No, I am saying that, if ToE is going to be claimed as the begin all, end all, it must do so. I am saying that we must look at ToE for what it is and isn't to understand life at all.
 
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rmwilliamsll

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Mitochondria are monophyletic. With the endosymbiont theory we would be lead to believe that they would be of polyphyletic orgin. This brings up a question as to the event itself.

why? if they have their origin in a single endosymbiont event would they be polyphyletic? i suspect problems with both terms monophyletic and polyphyletic here, they look like they are being used to refer to single point and multiple point origins, which i do not believe the used terms mean.
see:
http://en.wikipedia.org/wiki/Cladistics

but perhaps all it will take to be clear is some more words....maybe to expand what is meant here will help.
 
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Oncedeceived

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Ah, it is great to have internet again!!!
This link will exemplify why I feel that endosymbiont theory would lead us to a polyphyletic origin.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=99014

And that I am not the only one that believes this way:

Higher plants occupy very different positions in the mitochondrial and nuclear lineages of global phylogenetic trees based on conserved regions of small subunit (SSU) and large subunit (LSU) rRNA sequences. In the nuclear subtree, plants branch off late, at a position reflecting a massive radiation of the major multicellular (and some unicellular) groups; in the mitochondrial subtree, in contrast, plants branch off early, near the point of connection between the mitochondrial and eubacterial lineages. Moreover, in the nuclear lineage, plants branch together with the unicellular green alga Chlamydomonas reinhardtii, whereas in the mitochondrial lineage (in both SSU and LSU trees), metaphytes and chlorophyte branch separately. Statistical evaluation indicates that the anomalous branching position of higher plants in the mitochondrial lineage is not a treeing artifact attributable to the relatively rapid rate of sequence divergence of non-plant mitochondrial rRNA sequences. In considering alternative biological explanations for these results, we are led to propose that the rRNA genes in plant mitochondria may be of more recent evolutionary origin than the rRNA genes in other mitochondria. This proposal has implications for monophyletic vs. polyphyletic scenarios of mitochondrial origin and is consistent with other evidence indicating that plant mtDNA is an evolutionary mosaic.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=286893
 
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Lilandra

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I think RMWilliams was attempting to clarify what is meant by monophyletic and polyphletic because in terms of endosymbiosis the terms have 2 different contexts.

1. Yes, the origin of the mitochondial structure would be polyphyletic. Because of lateral genetic ransfers between different species of microorganisms, the structure is borrowed and shared between different lines polyphyletically.

2. But no, the origin of the microrganisms themselves cladistically speaking descended from a common ancestor.

Endosymbiosis can obscure the order of descent as genes are shared laterally.

A car analogy may help to illustrate this. Most cars have fuel injectors as the technology spread throughout different lines of cars. However whatever car had the fuel injector first doesn't necessarily reflect the origin of the first car, which others were modeled and revised from afterwards.

 
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I_Love_Cheese

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even better than you think, IIRC fuel injection comes from diesel engines from very early 1900's but wasn't used in cars and gasoline engines till late 50's though it may have been used in aircraft during WW2.

I'm sure some motorhead will tell me better though.
 
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Oncedeceived

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That is why I provided the link.
 
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