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Author Topic:   abiogenesis
Iblis
Member (Idle past 3896 days)
Posts: 663
Joined: 11-17-2005


(1)
Message 10 of 177 (543390)
01-17-2010 5:27 PM
Reply to: Message 1 by marc9000
01-17-2010 1:25 PM


Poetry and Biology
Abiogenesis is nothing less than a scientific analysis of what that "red clay" was composed of and what changes it underwent over time as God breathed that "breath of life" into it. Creation is nothing more than an inspired account of "Who done it."
The argument starts when people who can't understand poetry stake their faith and the faith of millions on obsolete pseudo-Aristotelian ideas about history and literary criticism. Aristotle wasn't popular with protein-starved churchmen because he was right, but rather because he had to dumb down his material to the point where even a bastard like Alexander the Great could get A's in his class.
Take it home, man. It was old and tired already before Jesus was born. God is dead; we killed him. He made us do it, because he was tired of shit like this. You can't be saved until you kill him too. In your heart, every day. Start now, give up your anti-science idol. They won't let you into heaven with these idols in your pockets. Kill it now.

This message is a reply to:
 Message 1 by marc9000, posted 01-17-2010 1:25 PM marc9000 has not replied

Iblis
Member (Idle past 3896 days)
Posts: 663
Joined: 11-17-2005


Message 23 of 177 (543630)
01-20-2010 12:41 AM
Reply to: Message 21 by Dr Adequate
01-19-2010 8:51 PM


Recognition
And yet I should think it a strange semantic quibble if someone were to argue that in that case, by definition, Jesus couldn't have turned water into wine; and stranger still if this argument came from a Biblical literalist.
They do say that though, in essence; or great gobs of them do, at least. They say that what he turned the water into was "new wine", alias grape juice, ie unfermented, aka won't get you drunk. They say this is why the wedding guests were so surprised that he didn't serve that first, but waited until they were all drunk and couldn't really appreciate the flavor and freshness of it. I know it makes more sense the other way around, but making more sense to the mature drinker isn't on their agenda anywhere.
http://www.biblestudymanuals.net/wine.htm
The difference between the denominations is really just a matter of recognition.
Catholics fail to recognize Protestants as fellow Christians.
Protestants fail to recognize the authority of the Pope.
And Baptists fail to recognize each other at the liquor store ...

This message is a reply to:
 Message 21 by Dr Adequate, posted 01-19-2010 8:51 PM Dr Adequate has not replied

Replies to this message:
 Message 25 by slevesque, posted 01-20-2010 3:04 AM Iblis has not replied

Iblis
Member (Idle past 3896 days)
Posts: 663
Joined: 11-17-2005


Message 27 of 177 (543642)
01-20-2010 3:20 AM
Reply to: Message 26 by Huntard
01-20-2010 3:12 AM


Re: A compromise, perhaps?
Haha no, that's the whole discussion! There's nothing to the question beyond the concession you just made!
If there had been, I would have posted something sensible about the primordial buffet by now.
PS: Oh, I guess there is the one dig about atheist bias, you could give that a good slapping. NM, carry on.

This message is a reply to:
 Message 26 by Huntard, posted 01-20-2010 3:12 AM Huntard has replied

Replies to this message:
 Message 29 by Huntard, posted 01-20-2010 3:27 AM Iblis has not replied

Iblis
Member (Idle past 3896 days)
Posts: 663
Joined: 11-17-2005


Message 67 of 177 (544052)
01-23-2010 1:38 AM
Reply to: Message 65 by marc9000
01-23-2010 12:24 AM


science please
I'll work on that, it may take a week, or it may take a month.
It's going to take longer than that. You will need falsifiable hypotheses, predictions, experiments, and replicable results. Abiogenesis has scores of these things, because the people interested in it are doing actual work instead of just trying to pit marketing against materialism.
Judge John E Jones III in Dover writes:
On cross-examination, Professor Behe admitted that: There are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred. (22:22-23 (Behe)). Additionally, Professor Behe conceded that there are no peer-reviewed papers supporting his claims that complex molecular systems, like the bacterial flagellum, the blood-clotting cascade, and the immune system, were intelligently designed. (21:61-62 (complex molecular systems), 23:4-5 (immune system), and 22:124-25 (blood-clotting cascade) (Behe)). In that regard, there are no peer-reviewed articles supporting Professor Behe’s argument that certain complex molecular structures are irreducibly complex.17 (21:62, 22:124-25 (Behe)). In addition to failing to produce papers in peer-reviewed journals, ID also features no scientific research or testing. (28:114-15 (Fuller); 18:22-23, 105-06 (Behe)). After this searching and careful review of ID as espoused by its proponents, as elaborated upon in submissions to the Court, and as scrutinized over a six week trial, we find that ID is not science and cannot be adjudged a valid, accepted scientific theory as it has failed to publish in peer-reviewed journals, engage in research and testing, and gain acceptance in the scientific community. ID, as noted, is grounded in theology, not science. Accepting for the sake of argument its proponents’, as well as Defendants’ argument that to introduce ID to students will encourage critical thinking, it still has utterly no place in a science curriculum. Moreover, ID’s backers have sought to avoid the scientific scrutiny which we have now determined that it cannot withstand by advocating that the controversy, but not ID itself, should be taught in science class. This tactic is at best disingenuous, and at worst a canard.

This message is a reply to:
 Message 65 by marc9000, posted 01-23-2010 12:24 AM marc9000 has not replied

Iblis
Member (Idle past 3896 days)
Posts: 663
Joined: 11-17-2005


Message 85 of 177 (544218)
01-24-2010 8:20 PM
Reply to: Message 83 by marc9000
01-24-2010 5:06 PM


Re: Explanatory power
http://www.studytoanswer.net/origins/abiogenesis.html
My question would be (and it’s not a challenge, just a question from myself, a non-scientist) does what you put forward above solve the reducing atmosphere problem as described in this link?
We normally refuse to debate websites, but we appear to be making an exception in this case specifically because your site is so ill-informative. In the future though, please cut-and-paste small portions and summarize relevant arguments in your own terms to make this a better experience for the readers.
Yes, the experiment successfully produced some amino acids, but it did so only as a result of the use of an atmosphere specifically engineered to yield amino acids, since simple molecules containing all the needed atoms were conveniently provided. Evolutionists justify the use of this atmosphere on the basis of their claim that the "early earth" had a reducing atmosphere (one lacking oxygen or other oxidising agents). Yet, the sole reason that this reducing atmosphere is proposed is so that they can then use it to justify their theories! Instead of searching for evidence and then revising their theories to the data, they were (and are) engineering the (proposed) conditions to yield the data they desired. The "reducing atmosphere" of the early earth is completely an evolutionist construct.
This shows a clear failure to understand reduction and its meaning in the study of earth's biosphere. Free oxygen is not a normal condition in the universe! The reason is that hydrogen is ubiquitous, what we tend to think of as "empty space" is actually very diffuse hydrogen. Combine this with the sharp variances in temperature normal to such a near-vacuum, and you have a situation where any existing free oxygen tends to combine with hydrogen to become water vapor and then precipitate into ice. Water is a relatively stable molecule and retains its structure through various elemental states, becoming more complex as other items are dissolved in it.
Several of the "soup" simulations I have witnessed started with free oxygen. It doesn't make any difference, the effect of the electrical discharge is to combine it with the abundance of hydrogen provided to increase the amount of water in the tank. There is no free oxygen left at the water level at the point where the amino acids begin forming.
Your site makes similar mistakes in understanding ultraviolet light; only they aren't mistakes, they are intentional deceptions.
Interestingly, if there had been an early reducing atmosphere when this abiogenesis was going on, the lack of an ozone layer would have meant that any amino acids formed in the primitive atmosphere would have been almost immediately destroyed by the intense ultraviolet radiation. Thus, it's a lose-lose situation for evolutionists on this count.
This is false on two counts. First of all, reduction by natural oxidation of hydrogen to produce a watery surface doesn't preclude the existence of O3 at a much higher elevation, where it could form an ozone layer. But beyond this, and more importantly, the penetration of large amounts of ultraviolet to the surface is not only not bad for the experiment, its essential, because uv at positive angles degrades right-handed compounds to a greater extent than it does left-handed, providing one key part of the best explanation for chirality.
We know that your site is aware of this second part, and ignoring it to confuse the issue, because they discuss it later in a weird misrepresentation of circular polarization in nebulae. Nor are their further arguments any more honest.
There has been no evidence found for the existence of this same sort of "sludge" anywhere in the geologic column, even though it should have been produced abundantly and laid down systematically throughout the entire period during which evolutionists propose that the process of abiogenesis was occurring.
The "sludge" is a key ingredient in hypotheses for the development of metabolism such as the nearly-universal "sandwich" model for the production of lipids and bases. Nor is there any big mystery as to why it isn't stored in the geologic table, it's volatile, it degrades over short periods of time unless energy is provided in a closed environment to generate more stable complex chemicals.
So then, after a vast misconception of what Miller-Urey does, what's the one substantial modern theory we see dissected? The pitiful 40-year-old clay, which was never made for us at all, it was always made for you, the believer.
One of these routes is to rely upon certain types of organophilic clays which are proposed to have served as "directors" for the reactions needed to produce simple biologic molecules, first proposed by the Scottish chemist Cairns-Smith.
Alexander Graham Cairns-Smith found in working with clay that it had certain properties that were useful in explaining (not accounting for, just explaining) the sort of crystalization-and-solution behavior that peptides and bases would have had to go through to become structured enough to become life. He also favors a quantum model for human thought and various other "new age" non-science models; on the other hand he's a good chemist. His "clay" only caught on specifically because it mirrors the bible account in some ways, making it the most appealing model for popular propaganda literature like The Blind Watchmaker by Dawkins.
It was already known to be a dead end at the time it began being used to describe the sort of thing that would have to be true to get to the RNA world, the real theory it is used to spice up as an "alternative" for (read, different angle on.)

This message is a reply to:
 Message 83 by marc9000, posted 01-24-2010 5:06 PM marc9000 has replied

Replies to this message:
 Message 94 by marc9000, posted 01-26-2010 9:51 PM Iblis has replied

Iblis
Member (Idle past 3896 days)
Posts: 663
Joined: 11-17-2005


(1)
Message 107 of 177 (544547)
01-27-2010 12:19 AM
Reply to: Message 94 by marc9000
01-26-2010 9:51 PM


Supper's Ready
So to sum up what you've said, we’re there, with naturalistic abiogenesis? The PAH world hypothesis, combined with claims that the early earth atmosphere posed no threats to it becoming a starting point for evolution to begin, is now a solid theory? I haven’t seen it on the news. What am I not being told about that keeps naturalistic abiogenesis in its current position of only a hypothesis?
Oh, it's worse than that. The main question has been settled for more than 50 years.
In 1953, Stanley Miller and Harold Urey demonstrated that many simple biomolecules could be formed spontaneously from inorganic precursor compounds under laboratory conditions designed to mimic those found on Earth before the evolution of life. Of particular interest was the substantial yield of amino acids obtained, since amino acids are the building blocks for proteins.
In 1957, Sidney Fox demonstrated that dry mixtures of amino acids could be encouraged to polymerize upon exposure to moderate heat. When the resulting polypeptides, or proteinoids, were dissolved in hot water and the solution allowed to cool, they formed small spherical shells about 2 μm in diametermicrospheres. Under appropriate conditions, microspheres will bud new spheres at their surfaces.
Although roughly cellular in appearance, microspheres in and of themselves are not alive. Although they do reproduce asexually by budding, they do not pass on any type of genetic material. However they may have been important in the development of life, providing a membrane-enclosed volume which is similar to that of a cell. Microspheres, like cells, can grow and contain a double membrane which undergoes diffusion of materials and osmosis. Sidney Fox postulated that as these microspheres became more complex, they would carry on more lifelike functions. They would become heterotrophs, organisms with the ability to absorb nutrients from the environment for energy and growth. As the amount of nutrients in the environment decreased, competition for those precious resources increased. Heterotrophs with more complex biochemical reactions would have an advantage in this competition. Over time, organisms would evolve that used photosynthesis to produce energy.
Microparticle - Wikipedia
The Miller-Urey-Fox "soup to nuts" model shows that in virtually any reconstruction of early earth conditions, we are quickly going to arrive at proto-life that is capable of mutating and evolving. The questions that remain open are all about how something like that might have gotten to something more like this, nucleic-acid based life with a cell structure.
Before I get to the difficult parts that are still subject to heavy debate, I want to show you how the "sandwich" part works.
The concept of the primordial sandwich was proposed by the chemist Gnter Wchtershuser to describe the possible origins of the first cell membranes, and, therefore, the first cell.
According to the two main models of abiogenesis, RNA world and iron-sulfur world, prebiotic[1] processes existed before the development of the cell membrane. The difficulty with this idea, however, is that it is almost impossible to create a complex molecule such as RNA (or even its molecular precursor, pre-RNA) directly from simple organic molecules dissolved in a global ocean (Joyce, 1991), because without some mechanism to concentrate these organic molecules, they would be too dilute to generate the necessary chemical reactions to transform them from simple organic molecules into genuine prebiotic molecules.
To address this problem, Wchtershuser proposed that concentration might occur by concentration upon ("adsorption to") the surfaces of minerals. With the accumulation of enough amphipathic molecules (such as phospholipids), a bilayer will self-organize, and any molecules caught inside will become the contents of a liposome, and would be concentrated enough to allow chemical reactions to transform organic molecules into prebiotic molecules.
Although developed for his own iron-sulfur world model, the idea of the primordial sandwich has also been adopted by some adherents of the RNA world model.
Primordial sandwich - Wikipedia
Neither of these are just hypotheses anymore. Their explanatory power has made them theories, and they are used as a background for a great many current hypotheses. I will get to one of these in a moment, but I have some more things I want you to be aware of first. These are things we can already synthesize for ourselves.
Liposomes are used for drug delivery due to their unique properties. A liposome encapsulates a region on aqueous solution inside a hydrophobic membrane; dissolved hydrophilic solutes cannot readily pass through the lipids. Hydrophobic chemicals can be dissolved into the membrane, and in this way liposome can carry both hydrophobic molecules and hydrophilic molecules. To deliver the molecules to sites of action, the lipid bilayer can fuse with other bilayers such as the cell membrane, thus delivering the liposome contents. By making liposomes in a solution of DNA or drugs (which would normally be unable to diffuse through the membrane) they can be (indiscriminately) delivered past the lipid bilayer. There are three types of liposomes - MLV (multilamillar vesicles) SUV (Small Unilamellar Vesicles) and LUV (Large Unilamellar Vesicles). These are used to deliver different types of drugs.
Liposomes are used as models for artificial cells. Liposomes can also be designed to deliver drugs in other ways. Liposomes that contain low (or high) pH can be constructed such that dissolved aqueous drugs will be charged in solution (i.e., the pH is outside the drug's pI range). As the pH naturally neutralizes within the liposome (protons can pass through some membranes), the drug will also be neutralized, allowing it to freely pass through a membrane. These liposomes work to deliver drug by diffusion rather than by direct cell fusion. Another strategy for liposome drug delivery is to target endocytosis events. Liposomes can be made in a particular size range that makes them viable targets for natural macrophage phagocytosis. These liposomes may be digested while in the macrophage's phagosome, thus releasing its drug. Liposomes can also be decorated with opsonins and ligands to activate endocytosis in other cell types.
Liposome - Wikipedia
These are artificial cell membranes that we construct on a regular basis for our own purposes. That in itself wouldn't mean that they could just occur naturally, but luckily we already know they occur naturally, using mineral bases and "sludge", as detailed above.
We also construct our own nucleic-acid chains, from scratch, for similar purposes.
DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas PNA's backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The various purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. PNAs are depicted like peptides, with the N-terminus at the first (left) position and the C-terminus at the right.[1]
Since the backbone of PNA contains no charged phosphate groups, the binding between PNA/DNA strands is stronger than between DNA/DNA strands due to the lack of electrostatic repulsion. Early experiments with homopyrimidine strands (strands consisting of only one repeated pyrimidine base) have shown that the Tm ("melting" temperature) of a 6-base thymine PNA/adenine DNA double helix was 31 C in comparison to an equivalent 6-base DNA/DNA duplex that denatures at a temperature less than 10 C. Mixed base PNA molecules are true mimics of DNA molecules in terms of base-pair recognition. PNA/PNA binding is stronger than PNA/DNA binding.
Synthetic peptide nucleic acid oligomers have been used in recent years in molecular biology procedures, diagnostic assays and antisense therapies. Due to their higher binding strength it is not necessary to design long PNA oligomers for use in these roles, which usually require oligonucleotide probes of 20—25 bases. The main concern of the length of the PNA-oligomers is to guarantee the specificity. PNA oligomers also show greater specificity in binding to complementary DNAs, with a PNA/DNA base mismatch being more destabilizing than a similar mismatch in a DNA/DNA duplex. This binding strength and specificity also applies to PNA/RNA duplexes. PNAs are not easily recognized by either nucleases or proteases, making them resistant to enzyme degradation. PNAs are also stable over a wide pH range.
Peptide nucleic acid - Wikipedia
Now we are getting to the good part. Peptide nucleic acid has been proposed as a good example of the kind of thing that would have had to have been there prior to an RNA or DNA world such as we see early life consisting of.
Numerous problems exist with the current thinking of RNA as the first genetic material. No plausible prebiotic processes have yet been demonstrated to produce the nucleosides or nucleotides or for efficient two-way nonenzymatic replication. Peptide nucleic acid (PNA) is a promising precursor to RNA, consisting of N-(2-aminoethyl)glycine (AEG) and the adenine, uracil, guanine, and cytosine-N-acetic acids. However, PNA has not yet been demonstrated to be prebiotic. We show here that AEG is produced directly in electric discharge reactions from CH4, N2, NH3, and H2O. Electric discharges also produce ethylenediamine, as do NH4CN polymerizations. AEG is produced from the robust Strecker synthesis with ethylenediamine. The NH4CN polymerization in the presence of glycine leads to the adenine and guanine-N 9-acetic acids, and the cytosine and uracil-N 1-acetic acids are produced in high yield from the reaction of cyanoacetaldehyde with hydantoic acid, rather than urea. Preliminary experiments suggest that AEG may polymerize rapidly at 100C to give the polypeptide backbone of PNA. The ease of synthesis of the components of PNA and possibility of polymerization of AEG reinforce the possibility that PNA may have been the first genetic material.
Just a moment...
Note that this covers the components of PNA, not the assembly process itself. Though much easier than something like RNA, synthesis of PNA still takes some work. So there was some confusion as to how such stacking could have occurred in nature.
Then, starting in 2003 as new starseed transmissions interpreted from the Red Rectangle nebula led us to a deeper understanding of Polycyclic/Nuclear Aromatics, it became clear how this could occur easily.
It is known that polycyclic aromatic hydrocarbons are a likely constituent of the primordial sea. PAH's are not normally very soluble in sea water, but when subject to ionizing radiation such as solar UV light, the outer hydrogen atoms can be stripped off and replaced with a hydroxyl group, rendering the PAH's far more soluble in water.
These modified PAHs are amphiphilic, which means that they have parts that are both hydrophilic and hydrophobic. Thus when in solution, like lipids, they tend to self organise themselves in stacks, with the hydrophobic parts protected.
In this self ordering stack, the separation between rings is 0.34 nm. This is the same separation found in RNA and DNA. Smaller molecules will naturally attach themselves to the PAH rings. However PAH rings, while forming, tend to swivel around on one another, which will tend to dislodge attached compounds that would collide with those attached to those above and below. Therefore it encourages preferential attachment of flat molecules such as pyrimidine and purine bases. These bases are similarly amphiphilic and so also tend to line up in similar stacks. This ends up making an effective scaffold for a nucleic acid backbone to form along the bases.
A small change in acidity would then allow the bases to break off from the original stack of PAHs and so form molecules like RNA.
Polycyclic aromatic hydrocarbon - Wikipedia
Note that my favorite, PNA, is almost certainly not the earliest occurrence of a natural nucleic acid. That honor goes to GNA.
The 2,3-dihydroxypropylnucleoside analogues were first prepared by Ueda et al. (1971). Soon thereafter it was shown that phosphate-linked oligomers of the analogues did in fact exhibit hypochromicity in the presence of RNA and DNA in solution (Seita et al. 1972). The preparation of the polymers was later described by Cook et al. (1995, 1999) and Acevedo and Andrews (1996). The GNA-GNA self-pairing described by Zhang and Meggers is however novel, and the specificity of interaction well-demonstrated, the molecules themselves.
DNA and RNA have a deoxyribose and ribose sugar backbone, respectively, whereas GNA's backbone is composed of repeating glycerol units linked by phosphodiester bonds. The glycerol molecule has just three carbon atoms and still shows Watson-Crick base pairing. Interestingly, the Watson-Crick base pairing is much more stable in GNA than its natural counterparts DNA and RNA as it requires a high temperature to melt a duplex of GNA. It is possibly the simplest of the nucleic acids, so making it a hypothetical precursor to RNA.
http://en.wikipedia.org/wiki/GNA_(nucleic_acid)
Also note, and this may have bearing on your main theme, everything in this post since Miller-Urey is engaged in evolution. It reproduces, it changes over time, it undergoes natural selection. The only thing that keeps it from being "life" is a metaphysical objection to calling anything less than a complete cell by that name.
Abiogenesis proponents are to a man atheist. The atheist leanings of the current scientific community are comparable to the religious leanings of the ID community.
Nonsense. All the Jesuits and more than half the Charismatics and huge gobs of the Spiritualists of all stripes support abiogenesis or chemical evolution as the means by which their creator accomplished his work. Anyone who studies what I'm giving you and isn't stuck in their box misinterpreting the poetry to limit God's options somehow has no problem with this process. It is, as I have mentioned already, a good solid elucidation of the concept of the development of modern kinds from "red dirt" / pre-organic compost / product of metabolism / shit, on command, of its own accord in its own way, without direct interference required. This is the same process Genesis describes.
I’ve been opposed by several in the past as a group[not here] and been taunted for missing just one or two evenings, as the new posts from different angles continued to pile up.
Well, I for one am not going to taunt you for not answering. What I'm going to taunt you for, is for answering without bringing in this "science" that ID is allegedly doing or being or consisting of.
What I want are hypotheses, predictions, experiments, and replicable results. In case someone may have confused you about this, Buzsaw for example, I don't care about peer review. Bring me replicable results, and I can then, replicate them. I've been through variations on the soup dozens of times, and the sandwich twice. I'm hoping for a stacking experiment with PAH sometime in the next year or so, but there are difficulties working with the stuff because it's a health hazard. (Don't want your genes restacked, do you? Neither did the 9-11 babies.)
There's a huge misrepresentation of how peer review works going on in the non-science community, to reiterate. If you can find replicable results, we can start replicating. Being a humble patent clerk or an anonymous internet rat doesn't prevent that, peer review can begin right here. I've also been involved in Deluge Theory corpse-stacking experiments, with church elders who didn't want to just believe a lie. Any subject, any hypothesis, someone here can walk through it with you.
Edited by Iblis, : psychic attack by Jesuits shouting Rectangle RECTANGLE

This message is a reply to:
 Message 94 by marc9000, posted 01-26-2010 9:51 PM marc9000 has not replied

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