Abiogenesis anyone?

[IrishEyes]

FT beat me to it - Irish, you limit life to "beings with awareness", which I would say still implies a roundabout definition (all beings that are aware are also alive).

Ok, I see your point. I don't know how to get around that though. Any suggestions on how to word it better? I'm trying to avoid this turning into a debate about what life is or is not. If we can come to a quick concensus of 'life' without it taking over this thread, I'd be willing to go there. Can you give us a definition that would work for the purpose of this thread?

All beings that are aware are also alive? But does that imply that anything that is not aware is not alive? I don't think I said this, but maybe it was implied. I just don't want the 'life' debate on tis. I really want to hear what you guys think is the best explanation for abiogenesis.

Maybe we should agree on a definition of life first. But then again I'm not listed in your exclusive list of VIPs so I'll shut up now.

Gee, you sound almost jealous! You silly silly, of COURSE I'm interested in what you have to say. As for it being a list of VIPs, don't be that way. You are THE VIP here, and we all know it. In all seriousness, I was asking for the people I mentioned to respond because I'm sure that the first 4 on the list will probably have very strong opinions that are probably supported by facts. That's not to imply that your opinion would not also be supported by fact, of course. Aw shucks, Tormod, I'm SORRY your name wasn't on the list, I messed up, can you please forgive me?????

[TeleMad]

FreeThinker: One such is Sidney Fox's spontaneously formed microspheres. It is based on volcanic reactions, one of the strongly held early earth models. Fox later found proteinoids similar to those he had created in his laboratory in lava and cinders from Hawiian volcanic vents and determined that the amino acids present polymerized due to the heat of escaping gases and lava.

Concerning Fox's proteinoid microspheres, from my personal notes (haven't looked at this for some time)...

Thermal Synthesis (Proteinoids)
One of the primary reasons that amino acids will not combine spontaneously to form dipeptides in a watery medium (which is where most origin of life scenarios place such processes) is that their bonding is a dehydration synthesis reaction (a.k.a., a condensation reaction). In such reactions, a molecule of water is formed from the atoms of the two amino acids and that water molecule must be introduced into the surrounding aqueous solution. This is against the thermodynamically favored reaction, which would be to take molecules of water from the sea, ocean, or lake and use them to hydrolyze dipeptides (break then back down into two separate amino acids). One solution to this problem is to drive off the water in the immediate surroundings so that a water molecule can be ‘plucked’ from the amino acids and inserted into the surroundings. Heating mixtures of dry amino acids has proven successful in creating polypeptide chains because it serves dual purposes – it supplies the energy for the polymerization and evaporates any water produced during polymerization.

“Could the primeval amino acids have joined into peptides under prebiotic conditions? What
looked like a simple positive answer to this question was found in 1958 by the American
biochemist Sidney Fox, long of the University of Florida, now at the University of South
Alabama. His recipe: Just heat a dry mixture of amino acids for three hours at 170o C (338o F).
Water comes out and you get a plastic-like solid that, when ground and mixed with water, yields
up to 15 percent of its weight as a water-soluble product made, on average, of some fifty amino
acids joined together. To this product Fox gave the name proteinoid, a cautious choice since
proteinoids are far from having the regular chainlike structure of peptides.” (Christian de Duve,
Vital Dust:Life as a Cosmic Imperative, Basic Books, 1995, p29)

But there are, of course, many problems with the thermal synthesis of “proteins”. First, objections to proteinoids themselves will be presented, followed by objections to the microspheres which they can form.

Proteinoids (objections to their relevance)
Another, this time more skeptical, background quote will be provided.

[quote]
“’Biochemists knew that when a mixture of amino acids in the ratio found in proteins was heated,
the result was pyrolysis to a dark brown tar with a disagreeable odor,’ commented chemist
William Day. At this point Sidney Fox made a contribution. Fox set aside the usual recipes and
added extra amounts of any of three special amino acids. These mixtures, when heated in the dry
state well above the boiling point of water, gave clean preparations, in which amino acids had
united with one another. The products obtained were not natural proteins, however, even though
they were made from amino acids. The special amino acids mentioned above contained either an
extra amino or an extra acid group. In normal proteins, these extra groups do not take part in
chain formation, but this had occurred in the heating process. Unnatural chains, even branched
chains, had been produced. Further, some of the amino acids had been converted into their mirror-
image forms, so both types were present. Others had been converted to colored substances,
pigments, which were also built into the chai

[TeleMad]

Hmmm...last post was too long...continued...

A further indication that proteinoid microspheres cannot synthesize their own protein is stated by Fox later in his book, in a section entitled Evolution from the Protocell to the Contemporary Cell:

“A more independent and adaptable cell arose, however, when some protocells acquired the ability to produce their own polyamino acids internally. These would have had to be a more contemporary type, in which the instructions from one generation to a descendant generation were channeled through the parents as individuals rather than being drawn from the monomers and their polymers in the environment.” (Molecular Evolution and the Origin of Life, Sidney W. Fox and Klaus Dose, W. H. Freeman and Co., 1972, p246)

One needs to keep in mind several points when he or she encounters a statement such as the following.

“Moreover, it is striking that amino-acyl adenylates yield oligopeptides when incubated with proteinoid-polynucleotide complexes, which thus have some of the characteristics of ribosomes.” (Biochemistry: Second Edition, Albert L. Lehninger, Worth Publishers, 1975, p1047)

First, the mentioned amino acids that join to form an oligopeptide are pre-activated – it is not the “protoribosome” itself that performs this task. In addition, the “protoribosome” was not composed simply of proteinoid – it also contained polynucleotides, which have not been synthesized under any plausible prebiotic conditions, let alone under those dry, high-heat conditions associated with proteinoid formation.

Cell-Like Membrane?
Cells have membranes in which phospholipids are the primary structural component, and in which membrane-spanning proteins transport materials across the barrier the membrane forms. However, the “membranes” of proteinoid microsphere are lipid-free and do not carry out the functions of cellular membranes.

“[Stanley] Miller and [Leslie] Orgel also criticize Fox’s statements relating microspheres to living cells. They state that the microsphere’s bilayer membranes “… are not ‘biological-like’ membranes since they do not contain lipids or carry out any of the functions of biological membranes.” They conclude, “It seems unlikely that … the division of microspheres is related to the origin of cell division.”” (Charles B. Thaxton [Ph.D. in Chemistry], Walter L. Bradley [Ph.D. in Materials Science], Roger L. Olsen [BS in Chemistry, Ph.D. in Geochemistry], The Mystery of Life’s Origin: Reassessing Current Theories, Lewis and Stanley, 1984, p175).

“Folsome criticized microspheres in that they possess a “grossly thick” boundary layer that more closely resembles a nearly impermeable cell wall or spore coat than a cell membrane.” (Charles B. Thaxton [Ph.D. in Chemistry], Walter L. Bradley [Ph.D. in Materials Science], Roger L. Olsen [BS in Chemistry, Ph.D. in Geochemistry], The Mystery of Life’s Origin: Reassessing Current Theories, Lewis and Stanley, 1984, p175).

Communication?
It is also claimed that proteinoid microspheres communicate by exchanging information-containing molecules.

“Inasmuch as the endoparticles [that move from the interior of one microsphere into another through a connecting, hollow proteinoid junction] are composed of proteinoid, and the proteinoid has been shown to be informational (page 174), the phenomenon constitutes a model for the origin of communication. This model relates to either intercellular communication or intergenerational communication; in fact, the phenomenon suggests the simultaneous origin of both types of communication (Hsu et al., 1971).” (Molecular Evolution and the Origin of Life, Sidney W. Fox and Klaus Dose, W. H. Freeman and Co., 1972, p217)

Although this claim of microsphere “communication” may be technically true, i

[IrishEyes]

Thanks for all of that, TeleMad.

I know that there is some outstanding information in there, and I greatly appreciate you supplying so many facts. Would it be possible for you to clearly and succinctly state your opinion of abiogenesis now? I DO appreciate all of the time and effort that you put into these posts, and I will keep all of this information to go over more thoroughly at another time. But I guess what I'm looking for is a plausible explanation for the development of living organisms from non-living matter? If it is in your posts, PLEASE let me know, because it totally went right over my head.

[Tormod]

Originally posted by: IrishEyes
Aw shucks, Tormod, I'm SORRY your name wasn't on the list, I messed up, can you please forgive me?????

Just wanted to hear it.

[Freethinker]

Originally posted by: TeleMad
Hmmm...last post was too long...continued...

Yes WAY too long. And did not need the continuation. I will retract my inclusion of Fox's experiments. Would have with a signficantly shorter post. I found it merely a curiousity regarding additional "Miller Tests".

[TeleMad]

Would it be possible for you to clearly and succinctly state your opinion of abiogenesis now?

How about, "I don't know"?

The RNA World theory has several advantages, the most obvious being that it helps break the chicken-or-egg problem. In all extant cells, DNA stores genetic information, RNA carries that genetic information to ribosomes, which are also made of RNA, and the information is used to synthesize proteins. The problem is, DNA cannot replicate itself....it requires proteins to do that. In addition, RNA synthesis also involves proteins, so there's feedback and interconnections. So without DNA there's no proteins....without proteins there's no DNA...and without DNA and no proteins there's no RNA. If the three parts are interdependent and all are absolutely required, how did the system arise? Well, DNA is kind of uneeded in that RNA can store genetic information. It is possible to have RNA store information and have proteins made from that RNA and for proteins to make the RNA. But that still leaves us with 2 parts that each requires each other. But in the 1980s, scientists discovered evidence of what others had speculated: RNA can also catalyze chemical reactions (catalytic RNAs are called ribozymes)...that is, they can act like proteins (but are far less impressive catalysts). So proteins too are not actually required....RNA could serve both the informational and the catalytic roles. Thus was born the RNA World theory. The key molecule of the RNA World is a self-replicating RNA molecule. There's one big problem for the theory. No experiment has produced an RNA replicase and the closest thing to date was a whopping 180 nucleotides long...and it could copy only 14 of its own nucleotides. The problem with a 180-nucleotide replicator (assuming the molecule actually could) is the low probability of one arising by non-directed ordering of nucleotides...there are 4^180, or about 2.35 x 10^108, possible unique sequences of that length; and even if a trillion of them could function as an RNA replicase, the probability of hitting one of those in a single shot is only about 1 in 2.35 x 10^96. The numbers can be played with some, but even assuming that a trillion trillion of those sequences could function as RNA replicases, the probability would still be only about 1 in 2.35 x 10^84. The second major problem with the RNA World theory is getting RNA! No prebiotic experiment has yet to produce even 1 RNA nucleotide.

[TeleMad]

Amino acids are easier to produce abiotically than is RNA, so maybe proteins were the first self-replicators. But proteins aren't synthesized the way nucleic acids are. In a nucleic acid (DNA or RNA), one strand serves as a template and, one at a time, the corresponding, complementary base binds on the growing strand. In protein synthesis, there is no template. mRNA holds the information for ordering the amino acids but getting the information out of the mRNA is a very complex task. So the process of protein replication is completely different and iunlike with RNA, nothing even close to protein replication viw amino acid polymerization has been found. The problem of genetic continuity arises - if the amino acids were joined without using templates, then each "generation" would be created anew, without reference to the previous "generation". Thus, there could be no evolution. Furthermore, it is actually RNA - not proteins - in the ribosomes that links the amino acids together during protein synthesis. Since proteins are much better catalysts than RNA, the most logical explanation is that RNA was the original linker of amino acids (if proteins were, then why would RNA have replaced them?). So this also suggests that RNA was there before proteins were.

[TeleMad]

Another possibility is that metabolism arose before replication. However, no prebiotic experiment has yet to produce a closed metabolic cycle that could be the beginnings of life. And Leslie Orgel states that there is no little reason to believe that such a close metabolic cycle could form in the absence of genetically encoded catalysts. So that would put us back to looking at RNA or proteins first.

[Freethinker]

Originally posted by: TeleMad

How about, "I don't know"?

The rest really didn't matter. When somone is looking for reasons to reject any particular Scientific principle or theory, just not having an absolute answer is all they want to hear. Becuase THEY can give you an absolute answer to any question you would be honest enough to admit "We don't know". It's the same answer to every question regardless and fails to fit every time. But they are looking for reasons to "believe" it and "We don't know" is good enough for them

The rest is just gibbly gook to them.

Abiogenesis, RNA, selfreplicators, ... Too complicated. Forget that this knowledge is saving lives in ways never imagined.

Just saw a story about how a man that lost his jaw bone to cancer generated his own new replacement. They took a computer simulation of what the bone needed to be shaped like and made a basic structure out of titanium. inserted his own stem cells into the frame. Surgically inserted it under his shoulder bone. It grew there into the needed bone with local muscle atrtached. Then then removed it from the back and relaced the missing jaw bone with it.

But it never happened because the knowledge for this to work came out of our understanding of Evolution and we know that Evolution is not only WRONG but EVIL!