The energetic origins of life

Jun 12, 2014 by John Hewitt report
Alkaline hydrothermal vents, like the Lost City, may have been key to origins of life. Credit: commons.wikimedia.org

(Phys.org) —Imagination is perhaps the most powerful tool we have for creating the future. The same might be said when it comes to creating the past, especially as it pertains to origin of life. Under what conditions did the energetic processes of life first evolve? That question is the subject of a remarkable perspective piece just published in Science. Authors William Martin, Filipa Sousa, and Nick Lane come to the startling conclusion that the energy-harvesting system in ancient microbes can best be understood if it is viewed a microcosm of the larger-scale geochemical processes of the day. In particular, they imagine a process by which natural ion gradients in alkaline hydrothermal vents, much like the "Lost City" ecosystem still active in the mid-Atlantic today, ignited the ongoing chemical reaction of life.

When it comes to origin of life discussions the so-called "RNA World" often comes to mind. While fascinating, that set of ideas is not what is under discussion here. According to the authors, it's all about the acetogens, the methanogens, and the chemical transformations that were key to their evolution. These microorganisms synthesize ATP using electrons from H+ to reduce CO2. In the process they generate either acetate or methane. The shared backbone in the energy metabolism of these microorganisms is the most primitive CO2-fixing pathway we know of—the acetyl-coenzyme A pathway. This pathway is generally referred to as the hub of metabolism as is links glycolytic energy production in the cell with oxidative energy production in its endosymbionts, the mitochondria.

While most acetogens are classified as bacteria, the methanogens belong to kingdom Archaea. This domain was only recently classified as distinct from bacteria and eukaryotes in 1977 by the late Carl Woese. Methogens are key to a bold leap of thought primarily made by Martin, which has come to be known as the "hydrogen hypothesis". Martin had seen a slide at a lecture which showed clusters of methogens inside eukarytoic cells nestled up right against hydrogenosomes, presumably feeding off the hydrogen they generate. Hydrogenosomes are similar to mitochondria in that they generate energy, put they are a paired-down version in that they do not contain any genome of their own.

Martin imagined that this cozy relationship he observed could have existed billions of years ago—only not as parasitic residents of a host eukaryotic cell, but rather as free residents at niche energy-producing locations within host earth. The host that then acquired what was to become the future mitochondrion was not a eukaryote with a fully-formed nucleus, but instead a prokaryotic and hydrogen-dependant methanogen. The future mitochondria then, was a facultative (as opposed to obligate) anaerobic eubacterium that in alternate incarnations also become the hydrogenosome.

The key feature and prediction of the theory is that the mitochondria created the nucleus, and therefore eukaryotes. This processes entailed massive transfer of most of the mitochondria's own genetic material to the host, which swelled the original genetic rank and congealed as chromosomes, simultaneously evolving the cyctoskeletal provisions for a complicated division cycle. The theory also neatly explains the lack of mitochondria in several eukaryotes through their loss, rather than as a failure to ever acquire them. The bio-existential question of whether the host "stole" the genes from the symbiont, or whether the parasite donated them becomes one of relativity and viewpoint. It is the same dichotomy as whether to say engulf or infect, or perhaps whether the assorted neurotransmitter packages dispensed by neurons are wastes, gifts or irritants.

Few researchers have done more than co-author Nick Lane towards uncovering the role of mitochondria in nearly every major process of the cell. He has summed up many of these ideas in his book Power, Sex, Suicide: Mitochondria and the Meaning of Life. In it he observes many things that like the hydrogen hypothesis, are now becoming accepted reality. Of note, he maintains that using those few genes preserved as local copies in the mitochondrial genome, different regions of the cell can rapidly tailor their energy output. In the case of the extended trees of neurons, this might also contribute to structural alterations and perhaps even memory.

As far as the origins of life, we need to turn back into the opposite direction now to try to un-create what might have happened prior to the eukaryotic merger, or at least led to it. In 2012 Martin and Lane published their thought-advances in imagining some of the geochemical processes which were later sped up, compacted, and made more efficient inside cells. These include how ion-gradients were set up at hydrothermal vents, bandied about, and later swapped H+ ions for Na+ ions as both the carriers and composers.

One such process they detail in their new paper is known as serpentinization. In this sequence of geochemical reactions, seawater percolating through submarine crust exothermically oxidizes Fe2+ to Fe3+ along with the release of H2 and energy. Serpentinization taking place at the Lost City formation, for example, generates a strongly reducing environment (reducing CO2), and it also makes the effluent alkaline with a pH of around 10, essentially controlling the fluid composition of the vent. Natural proton gradients are spontaneously set up with the same magnitude and orientation as occurs inside modern autotrophes (self-nourishing, producing cells).

What were the first ion-pumping mechanisms?

These vent features make them naturally chemiosmotic. In chemiosmosis, as also occurs in , ions flow down natural gradients which can potentially be harnessed to produce energy. In the case of life, which universally employs multi-tool pumps known as ATP-ases, this energy is deposited as phosphate bonds in ATP. If the primordial ATP-ase harnessed these alkaline vent gradients, a first step could have involved a simple H+/Na+ antiporter. This kind of a device (now also protein-based like the ATP-ase) could have converted the initial vent gradient into the Na+ gradient the acetogens and methanogens use today. These complexes still use iron-sulfer clusters and methyl groups as substrates, and could have enabled the emergence of free-living prokaryotes.

Our understanding of chemiosmosis today is still incomplete. The so-called "proton-motive force" which couples proton and electron transfer across nebulous barriers still defies exact quantification. The flow of electrons through proteins, and the membranes which house them, continues to be one of the most exciting areas both in the origins of life, and in the creatures later evolved.

Explore further: New study outlines 'water world' theory of life's origins

More information: Energy at life's origin, Science 6 June 2014: Vol. 344 no. 6188 pp. 1092-1093. DOI: 10.1126/science.1251653

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discouragedinMI
Jun 12, 2014
This comment has been removed by a moderator.
verkle
1 / 5 (21) Jun 12, 2014
Unbelievable! Now looking for origins in alkaline hydrothermal vents? Scientists gone berserk!
hrfJC
1.3 / 5 (26) Jun 12, 2014
This lifelong industrial scientist utilizing scientific facts must categorically reject such idle philosophical speculations regarding the origin of life by conversion of inorgsnic primordial mud to unicellular self replicating or living cells by unknown processes defying known natural laws. This would require a quantum leap of blind faith normally attributed to creation by an omniscient software programmer and engineer. The proposed prebiotic reactions must virtually simultaneosly generate the multiple interlinked interactions of hundreds of organic entities uniquely interacting with specific complementary enzymes, depicted in the classical chart of Metabolic Pathways known to all biochem majors, to create living cells. Clearly a statistically improbable if not impossible process in the required brief time span, since sequential formation is not an option to produce life in a longer time frame. Meaning all these idle ruminations are totally unscientific, hence are faith based.
verkle
1.2 / 5 (22) Jun 12, 2014
hrfJC, well said.
animah
4.8 / 5 (21) Jun 13, 2014
statistically improbable (...) must simultaneosly generate (...) living cells

Improbable if AND ONLY if life cannot be a progressive physico-chemical process occurring in the +enormous+ volume of this Earth with trillions of chemical reaction at any given time over hundreds of millions of years.

Improbable if AND ONLY if life must instead pop-up fully formed, like there is some physical law that demands instantaneous assembly.

There isn't. The odds are just fine. Faith not required.

But no! You think the explanation is in an iron age collection of short supernatural stories riddled with stupidities requiring all kinds of highly subjective interpretations.

Furthermore, you think your highly subjective interpretation is better than other people's, and that makes you superior.

You're pathetic.

I think admitting we don't know much and are still looking, spending a lifetime studying nature trying to find answers, and in so doing discovering cancer cures is heaps better. Fool.
nowhere
5 / 5 (15) Jun 13, 2014
regarding the origin of life by conversion of inorgsnic primordial mud to unicellular self replicating or living cells by unknown processes defying known natural laws.

You are being dishonest when you misrepresent the opposing view by purposefully excluding the connecting processes between the two stages of life formation, which essentially forms the entirety of the subject you are arguing against.
antialias_physorg
5 / 5 (19) Jun 13, 2014
defying known natural laws

I'm curious: which known natural law does this defy?
And please don't give any vague psycho-babble. Give hard laws that are testable. Since they are (as you claim) 'known' that should be quite easy for you to do.
rafatom
1 / 5 (7) Jun 13, 2014
You can see a full documentary on this here:
https://www.youtu...y6KJuKhs
hrfJC
1.4 / 5 (9) Jun 13, 2014
Look at a downloadable copy of the Metabolic Biochemical Pathways showing the complex networks of interlinked substrates and their specific enzymes that are absolutely essential to living cells.Even a single alteration in a critical metabolic cycle may cause cell death.Also read the review of several proposed primordial evolutionary pathways in open access PLoS Biology 6:5-13, 2008 by Leslie Orgel entitled The Implausibility of Metabolic Cycles on the Prebiotic Earth concluding with.... they are dependent on speculative "" if pigs could fly" chemistries that are akin to the geothermal hypotheses.
MrVibrating
2 / 5 (6) Jun 13, 2014
@antialias

Just ignore the zombies. If they had ANY real sense of the sacrosanct they'd realise the depths of their antropomorphic blasphemies and spend the rest of their days doing useful penance in a lab somewhere. Besides, the longer they spend reading here and TRYING to think clearly, the sooner they'll realise their ant-god can't cut it, and start really appreciating the gifts of existence.
Torbjorn_Larsson_OM
5 / 5 (6) Jun 13, 2014
Interesting to see the Martin-Lane vs Russell split. Russell, the grand old man of vents leaft these ideas (still co-authoring with Martin 2010) sometime before 2013 when he held his SETI seminar. [Youtube]

Apparently the methanogen/acetogen coevolution hypothesis got backlash from phylogeneticists, despite these lineage being ancient. Indeed, there are papers that point to non-chiral lipid membranes of the UCA with the Archaea/Bacteria (opposite chirality membranes) split later.

Russell et al new CO2/CH4 root metabolism seems much more fruitful. No need for complex protein coevolution antiporters, instead simplest possible electron bifurcating atoms (Mo, say) did the chemiosmosis driven deed. And, even if Russell may not yet have gone there himself, his acetyl metabolism bootstraps nicely the recent spontaneous glucolysis pathway Keller et al found. (Since Russell's semipermeable membrane protocells can reverse that to the gluconeogenesis metabolism.)
Torbjorn_Larsson_OM
4.6 / 5 (11) Jun 13, 2014
Creationists still trolling science site with the failed "too complex root" idea? Despite evolution predicts how complexity is a result of previous simplicity. When e.g. Shostak's protocells have _two_ components until life, both spontaneously emerging and assembling. Children can count to two, apparently creationists can't. Who are the fracking morons? =D

1. We know that life emerges out of geophysics, because of history. Early life was lifeless, now it has life, hence geophysical emergence.

2. We know that chemical evolution, which consists of small chemical changes, continues into biological evolution, which consists of small survivable changes.

3. And everybody should know that Martin & Lane suggested a homology between submarine alkaline hydrothermal vents and modern cells, a trait phylogeny as it were. Hence the current examples, such as Lost City, are our most distant cousins.

[tbctd]
supamark23
5 / 5 (9) Jun 13, 2014
Look at a downloadable copy of the Metabolic Biochemical Pathways showing the complex networks of interlinked substrates and their specific enzymes that are absolutely essential to living cells.Even a single alteration in a critical metabolic cycle may cause cell death.Also read the review of several proposed primordial evolutionary pathways in open access PLoS Biology 6:5-13, 2008 by Leslie Orgel entitled The Implausibility of Metabolic Cycles on the Prebiotic Earth concluding with.... they are dependent on speculative "" if pigs could fly" chemistries that are akin to the geothermal hypotheses.


Yeah... that stuff evolved over, literally, billions of years and not all organisms share the same metabolic pathways. One thing's for sure though, you're an idiot.
Torbjorn_Larsson_OM
4.6 / 5 (10) Jun 13, 2014
[ctd]

That biological methods covers Hadean geophysics is a triumph for astrobiology. It means that we know the pathways taken as much as we know other pathways in the tree of life.

So no, people are still studying the emergence of life. But we are no longer searching for the correct pathway. We are weeding out the remaining incorrect that people hanker to. (E.g. Shostak's protocells doesn't look too good.)
Torbjorn_Larsson_OM
4 / 5 (8) Jun 13, 2014
Re: "Also read the review of several proposed primordial evolutionary pathways in open access PLoS Biology 6:5-13, 2008 by Leslie Orgel entitled The Implausibility of Metabolic Cycles on the Prebiotic Earth concluding with.... they are dependent on speculative "" if pigs could fly" chemistries that are akin to the geothermal hypotheses."

A reference! Good for you. But it is dated, already 6 years old. Let's see if it is still relevant:

So have I read that earlier. It doesn't really bear on Shostak's protocells, who are non-metabolic theories. It also doesn't conflict much with the later (2010 and forward) root metabolic pathways of Martin & Lane or Russell et al, since they are simple (no branching) and often lab verified.

[tbctd]
Torbjorn_Larsson_OM
4.1 / 5 (9) Jun 13, 2014
[ctd]

However, imagine my surprise when Keller et al recently showed Orgel wrong on more complex 3-6 C metabolism. You can only do it with using modern analysis equipment, in fact only one method works so far.

But using that, Keller et al could show that non-enzymatic metabolism appears in plausible Hadean (or Archean) anoxic Fe(II) rich oceans. (In fact, modern oceans would do a small subset.) They note that Orgel (et al, there are more papers like his) ideas on metabolism-like chemical reaction sequences being unlikely has never been tested systematically. Nor can thermodynamic approaches yet predict their likelihood.

[tbctd]
Torbjorn_Larsson_OM
4.1 / 5 (9) Jun 13, 2014
[ctd]
But they work, they use metal atoms for the chain and ... _they are as efficient as modern pathways (30 % vs 25 % product after 29 [!] steps)_ ! (They are however much slower, at least without cell like crowding. But that is not a problem for protocells.) Of course, since there were no chirality, the efficiency starting with non-chiral material (see my acetyl suggestion) is halved. But the point is that _Orgel was wrong_ and _Orgel was speculative_. And that his particular pig won't fly ever again.

["Non-enzymatic glycolysis and pentoise phosphate pathway-like reactions in a plausible Archean ocean", Keller et al, Molecular Systems Biology. 2014]

Also, a word of advice: trying to criticize something, and creationists do nothing else because they have no plausible alternative mechanism to chemical evolution, one must keep up with the subject. If you fail to do so you show how little it interests you, and how little your claims mean. E.g. "One thing's for sure though, ..."
Torbjorn_Larsson_OM
3.9 / 5 (7) Jun 13, 2014
Oy! I meant pentose, not "pentoise".

Also, re the remarkable efficiency, that's not all in the paper but the rest in a point in the review notes (with references) linked at the paper.
Torbjorn_Larsson_OM
4 / 5 (9) Jun 13, 2014
"one must keep up with the subject."

Ha! I checked, and to no surprise to anyone, the Orgel paper (but presumably not the later ones on the same theme) are now used by creationist sites as some sort of magic formula.

It will be interesting to see, as the news of Keller et al advance spreads, if creationists will make the note "do not use this argument" at Orgel's piece. Some of their sites try to keep their magic agency apologetics from using obvious errors.

But it never takes. (E.g. that is why we still see the inane "too complex root" despite that the simplicity of the root is both implicit in the process (coming from even simpler geophysics and moving towards more complex modern cells) and explicit in the found pathways (Shoztak, Martin & Lane, Russell, ...).
Vietvet
3.9 / 5 (7) Jun 13, 2014
@Torbjorn Laesson OM

Your comments make it worthwhile reading the slime put out by the science deniers.
hrfJC
1.3 / 5 (12) Jun 13, 2014
From your comments and format i perceive you critics do not know biochemistry as I do as an industrial scientist and thus cannot grasp the significance of Orgel 2008 and the timelessnes and proven accuracy of the Metabolic chart governing most living cells. To deny the validity of this scientific chart betrays extreme ignorance and/or hopeless myopia and if correct you would be dead right now.. Also use of Orgel by creationists does not invalidate his observations and critcism just like my using a Marxist argument does not make me a communist. I pity some of you mired in a sea of wild non scientific speculations peppered with "we know" when in reality you and indeed no one else knows. And with this comment I sign off since you are close minded and unteachable.
animah
4.5 / 5 (8) Jun 13, 2014
Ha! And yet when thoughtful debate around Orgel's research occurs as is normal in the process of advancing knowledge, you offer... Deafening silence. None of you can participate in the scientific conversation.

You desperately want history to freeze frame at that one drop of ink.

Someone told you his paper could be misinterpreted to fit your iron age book, and you took the bait.

The utter stupidity of applying the metabolic chart of today's organisms, with their complexities refined for hundreds of millions of years, to the time the building blocks of life were just starting to interact, is not even apparent to you.

You're just being left behind as the man-child wannabes you guys are.
animah
4.3 / 5 (6) Jun 13, 2014
To clarify on Orgel who was (wait for it...) and evolutionary biologist!

The paper ignorant hrfJC refers to catalogues research areas Orgel felt his colleagues should focus on going forward, because he knew he was dying. That his legacy shoud be misused in this way is heart breaking. Way to go Xians.

Here is the conclusion from his paper, his last words to the scientific community. Make up your own minds:

(cont below)
animah
5 / 5 (5) Jun 13, 2014
Leslie Orgel: The Implausibility of Metabolic Cycles on the Prebiotic Earth

Published posthumously

http://www.plosbi....0060018

The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. (...). No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on "if pigs could fly" hypothetical chemistry are unlikely to help.
Captain Stumpy
4.6 / 5 (11) Jun 13, 2014
From your comments and format i perceive you critics do not know biochemistry as I do as an industrial scientist
@hrfJC
IF you are actually an industrial scientist, and cannot comprehend the conversation that Torbjorn_Larsson_OM just gave you, which not only refutes your proposal, but destroy's your argument, then I would have to say that you are more like jvk in that you are denying empirical evidence for the sake of a philosophy that is not only unsupported, but also proven fallacious
And with this comment I sign off since you are close minded and unteachable
it is good to run and hide! here you will only find pain because you will find people who are actually well versed in science refuting you, not laymen who will cower before your appeal to your own supposed authority.

thank you for leaving.
there is no use for religion in science, and no use for stupid here either.

Thank you Torbjorn_Larsson_OM for those great posts, and animah for the info on Orgel
adave
1 / 5 (9) Jun 13, 2014
From the time of the first synthesis of life, we should find a layer of sediment built up where life had been generating from inanimate minerals. That would have continued until the oxygenation of the biosphere. Even if the origin of life is off the planet, we should still have very primitive sediment layers since they should be able to compete with more complex symbiotic life over geologicly significant time. That implies that life started on the earth in an advanced state skipping the early evolutionary stages. Panspermia would be the answer by a large meteor from an methane CO2 atmosphere planet generating or falling near a geothermal vent. The rock with life blasted off another planet would have to be living subducted sediment just like on earth with tectonics and an ocean. Bacteria can survive enormous deceleration. Fragmentation and erosion would expose a large surface. How far back in time? What other solar system exchanged mass with our own 4.5 billion years ago?
Captain Stumpy
4.5 / 5 (8) Jun 13, 2014
we should still have very primitive sediment layers since they should be able to compete with more complex symbiotic life over geologicly significant time. That implies that life started on the earth in an advanced state skipping the early evolutionary stages
@adave
And you have empirical evidence supporting this conclusion?
would you mind sharing those links and references?
Whydening Gyre
4.5 / 5 (8) Jun 14, 2014
It appears to me, as an uninformed layman, 'life' is an unintended consequence of carbon's unique ability to chemically bond with - well just about anything. It is likely one of the most prolific atomic structures, in that regard.
Not stating a theory or anything. Just an observation.
feath3r
1 / 5 (5) Jun 16, 2014
Shostak's protocells have _two_ components until life, both spontaneously emerging and assembling.

Torbjorn_Larsson_OM,
I assume you meant to say Szostak. Are your "two components" by any chance (1) self-replicating genetic polymer and (2) self-replicating membrane boundary?

If so, I must say that you're being dishonest to sound as if those two components are something that could have emerged unchallengingly. Let's make it clear that no protocell has ever been created in a laboratory yet.

According to "The Origins of the RNA World" published by Robertson and Joyce:
"It is not sufficient, however, that there be just one copy of a self-replicating RNA. The above calculations assume that a self-replicating RNA can copy itself ... If two or more copies of the same 40mer RNA are needed, then a much larger library, consisting of 10^48 RNAs and weighing 10^28 g would be required. This amount is comparable to the mass of the Earth."

In short, self-replication = highly improbable
animah
5 / 5 (5) Jun 16, 2014
you're being dishonest

No, +you+ are being dishonest in the extreme. "The Origins of the RNA World" is also available online, readers make up your own minds:

http://www.ncbi.n...3331698/

Your quote is completely out of context. The authors are in the middle of demonstrating the case FOR the RNA world and in fact destroying your iron age dogma.

2 lines before:

"... even a small fraction of the total library, consisting of perhaps 1020 sequences and weighing about 1 g, might be expected to contain at least one self-replicating RNA with the requisite properties."

10 lines later:

"... then it is not difficult to imagine how RNA-based evolution might have started"

And as the demonstration progresses:

"... the RNA World would have been on solid footing"

If ignorance is bliss, you must be orgasmic.
feath3r
1 / 5 (6) Jun 17, 2014
animah,
Please read the entire paper. The very next section says:
"The previous discussion has tried mightily to present the most optimistic view possible for the emergence of an RNA replicase ribozyme from a soup of random-sequence polynucleotides. It must be admitted, however, that this model does not appear to be very plausible. The discussion has focused on a straw man: The myth of a small RNA molecule that arises de novo and can replicate efficiently and with high fidelity under plausible prebiotic conditions. Not only is such a notion unrealistic in light of current understanding of prebiotic chemistry (Joyce 2002), but it should strain the credulity of even an optimist's view of RNA's catalytic potential."

The paper is written by RNA World experts. If you read the entire paper, you will see that they basically describe all hypotheses of abiogenesis, including their RNA World, and point out their unsolved challenges for each one of them, because none of them are realistic yet.
animah
5 / 5 (6) Jun 17, 2014
I have read the entire paper and more.

The authors explore a number of possible existing lines of research, make compelling arguments against some and compelling arguments in favour of others.

2 in fact just after the sections you cherry-picked, where he says first:

"... under such conditions of segregation, evolutionary bootstrapping can occur, resulting in progressively larger genomes"

And then:

"Alternatively, the requirement for replication of related, but not unrelated, sequences might be met through the use of "genomic tags" (Weiner and Maizels 1987)".

One of the authors, Joyce, even spoke out against you creationist ignorants misusing his reseach (and so did Orgel):

http://www.arn.or...2003.htm

Instead of being born again, why don't you just grow up?
feath3r
1 / 5 (5) Jun 17, 2014
animah,
You think the arguments are so "compelling"? Let's hear from the authors' conclusion:

"After contemplating the possibility of self-replicating ribozymes emerging from pools of random polynucleotides and recognizing the difficulties that must have been overcome for RNA replication to occur in a realistic prebiotic soup, the challenge must now be faced of constructing a realistic picture of the origin of the RNA World. The constraints that must have been met in order to originate a self-sustained evolving system are reasonably well understood. One can sketch out a logical order of events, beginning with prebiotic chemistry and ending with DNA/protein-based life. However, it must be said that the details of this process remain obscure and are not likely to be known in the near future."

Again, "remain obscure and are not likely to be known in the near future."

Does that sound "compelling" to you?

Unlike you, the authors are being honest and admit on no realistic hypothesis yet
animah
5 / 5 (5) Jun 17, 2014
The constraints that must have been met in order to originate a self-sustained evolving system are reasonably well understood. One can sketch out a logical order of events, beginning with prebiotic chemistry and ending with DNA/protein-based life.


Exactly. Work continues. We are as far as can be from your childish creationist "self-replication = highly improbable" drivel.
Captain Stumpy
5 / 5 (6) Jun 17, 2014
However, it must be said that the details of this process remain obscure and are not likely to be known in the near future.
@feath3r
If I may interject: there is another POV that you are not considering with this statement, feath3r. Judging from the paper and from the entire concluding remarks, it appears IMHO that the authors are saying something more along the lines of: they have a good grounding and met the constraints but have not replicated the conditions specific of early earth and generated the RNA conclusions except in models etc.

Exactly what POV are you pushing for here? Are you trying to justify creationist?
feath3r
1 / 5 (6) Jun 17, 2014
Captain Stumpy,
Actually the paper does not say that they have "met the constraints". It says that they understand what constraints must have been met - meaning the current models do not meet the constraints yet as the paper explains.

The POV that I am trying to make is that currently there is no realistic model of abiogenesis yet. We speculate what the milestone events must have been, but we cannot explain how those events could have occurred in nature.

I respect Joyce and Orgel because they are honest. They are being a true scientist by self-criticizing even their own hypothesis because it is found to be unrealistic. What I don't appreciate is people like Torbjorn_Larsson_OM and animah who try to make it sound as if we know the answer when we don't.
animah
5 / 5 (5) Jun 17, 2014
I am not trying to make it sound as if we know the answer. In fact I even said above:

I think admitting we don't know much and are still looking, spending a lifetime studying nature trying to find answers, and in so doing discovering cancer cures is heaps better.


What you are doing is very different with:

criticizing even their own hypothesis because it is found to be unrealistic


By replacing "incomplete" or "work in progress" with "unrealistic", you are trying to create a false record that Robertson, Joyce and Orgel have somehow disproved abiogenesis, for use in creationist literature. I know because I checked.

So just to set the record straight: Nothing could be further from the truth. The scientists in question even had to intervene to stop this dishonest practice.
feath3r
1 / 5 (7) Jun 17, 2014
By replacing "incomplete" or "work in progress" with "unrealistic"

animah,
1. Are you trying to say that the work is in progress, in addition to having a realistic answer?? No. the work is in progress BECAUSE there is no realistic answer. in other words, all currently proposed answers are unrealistic.

2. Please quote me where I said, "Robertson, Joyce and Orgel have somehow disproved abiogenesis." I have never said that, so I would appreciate it if you don't put words in my mouth. What I said was that even they acknowledge that currently there is no realistic answer (which is true).

3. What is up with your obsession with creationist? Have I ever used the word Creationism here? Please don't keep putting up a straw man. Again my issue is with people who present a false impression that the current science has a realistic answer. It does not.

Well, it sounds like you're admitting there is no realistic answer on abiogenesis. So, I think we are in agreement. Goodbye.
animah
5 / 5 (4) Jun 17, 2014
all currently proposed answers are unrealistic

This is the free world, so you are entitled to your opinion.

But Robertson, Joyce and Orgel disagree with you. Their research says the opposite of what you say. They have forefullty stated that in public.
feath3r
1 / 5 (5) Jun 17, 2014
animah,
Please make up your mind; you are contradicting yourself in your two previous posts.

Again, this is how Robertson and Joyce concluded their paper.
"After contemplating the possibility of self-replicating ribozymes emerging from pools of random polynucleotides and recognizing the difficulties that must have been overcome for RNA replication to occur in a realistic prebiotic soup, the challenge must now be faced of constructing a realistic picture of the origin of the RNA World. ... However, it must be said that the details of this process remain obscure and are not likely to be known in the near future."

"... the challenge must now be faced of constructing a REALISTIC picture..."

Does that sound to you that there is a single realistic answer?
animah
5 / 5 (4) Jun 18, 2014
No. You are the one who is misusing their words.

They are saying, literally, that we are now recognizing the difficulties of making a theoretical model for a realistic prebiotic soup.

So making life is difficult. Big insight LOL - it's obvious: life is rare in the universe.

Difficult has nothing to do with what you are trying to peddle, which is that is couldn't have happened naturally.

The universe is so big that improbable things happen all the time. It's perfectly natural. Like Vegas or the lottery :-)
feath3r
1 / 5 (5) Jun 18, 2014
animah,
I asked you a simple question that requires a simple Yes/No reply.

Again, does that sound to you that there is a single realistic answer?

The universe is so big that improbable things happen all the time. It's perfectly natural.

That depends on the improbability. Look up "Boltzmann brain" and you will understand that even the universe is not big enough for certain events.

For abiogenesis, we know the universe is not big enough for DNA/Protein World to have occurred initially, which is why RNA World was introduced. However, as Joyce calculated, RNA World requires RNA library "comparable to the mass of the Earth." Obviously, Earth has never hosted RNA library as heavy as itself, so the size of the universe is irrelevant.

As you said, this is the free world, so you are entitled to your opinion. But don't pretend for a moment that your belief on the improbability is based on science. If you want to be truly scientific, then your answer should be, "I don't know."
animah
5 / 5 (3) Jun 18, 2014
No. Joyce and Robertson are comparing various scenarios proposed by colleagues. They offer various arguments around them, and the "mass of the Earth" critic is for ONE OF these various scenarios, NOT ALL.

I agree with Joyce, Robertson and Orgel: We don't know yet, and constructive work continues to progress towards an answer. It will take time.

I disagree completely with you that it's not possible based on your childish simplification.

The answer to your question: Is there a realistic answer? is YES. We'll find it. That much, the entire biologist community agrees with.
feath3r
1 / 5 (3) Jun 18, 2014
I disagree completely with you that it's not possible.

animah,
I warned you before - don't put words in my mouth. Find the quote where I said "not possible". You can't, because I never said it. I am beginning to see why you have such comprehension problem.

And don't play with words. You know very well the question was if there was a realistic answer that science has discovered already (no, there is none), not if science would find the answer in the future (which is a speculative belief).

Yes, I've been telling you over and over, and you finally admit it - Joyce, Robertson and Orgel said that we don't know yet. That's the fact of the current science. Don't try to add your personal belief on top of that and try to sell it as the scientific fact.
animah
5 / 5 (3) Jun 18, 2014
"Speculative belief": An expression only a certain small interest group in the entire world uses in this context. All is clear.

It's a pretty shallow strawman too. Let me explain. You said:

That depends on the improbability. Look up "Boltzmann brain"


See, that idea is a hypothetical mind experiment. It's not found in nature. You are ignoring the single most important learning of the last 200 years of science:

No scientific research has ever shown any observed phenomena of nature to be impossible or to break the laws of physics, thus requiring supernatural intervention. NOT ONE among tens of millions of findings over 2 centuries.

Thus there is no reason at all to believe we won't find the answers. None.

Now we don't know everything, that's for sure!

But undiscovered <> disproved.

This leaves you with the god of the (narrowing) gaps.

That's fine with me. So long, child.
Sikla
Jun 18, 2014
This comment has been removed by a moderator.
feath3r
1 / 5 (5) Jun 18, 2014
See, that idea is a hypothetical mind experiment. It's not found in nature.

animah,
You first said, "The universe is so big that improbable things happen all the time. It's perfectly natural." So, I told you to look up Boltzmann brain. Do you know why it's not found in nature? Because it is highly improbable. Too improbable that your "big universe" doesn't save you. Your usage of "big universe" as some kind of a magical answer to all improbable questions is what a non-scientist would do who does not understand the issue.
But undiscovered <> disproved.

What is wrong with you? Stop putting words in my mouth!! You can't comprehend because you can't even distinguish what others said.
But, you said it, not me. Think about what you said and you will slowly realize that you just argued FOR creationists you so hate. LOL
animah
5 / 5 (3) Jun 18, 2014
You missed the point. We come up with useful mind experiments all the time. Because they are mind experiments, they can have any "what if" components, however improbable or even impossible.

But life is an observable phenomenon. It is therefore NOT improbable.

This is the key learning I was talking about. In 200 years, nothing found in nature was shown to require more than logic to explain. That's why science is demonstrably not a religion.

That's why the idea of a "speculative belief" that we will find realistic answers is bogus. Knowledge is a function of time; there are no hidden variables. We'll find the answers.

So when you say
you just argued FOR

You are welcome to your Delusion LOL. Really though, your ideas are so completely aligned to ID, you shouk stop pretending and have the courage to "come out".
feath3r
1 / 5 (5) Jun 18, 2014
But life is an observable phenomenon. It is therefore NOT improbable.

I know why you are so confused now. It makes perfect sense - you're not a scientist. That's why you use the word, "improbable", interchangeably with "impossible". And why you don't comprehend what you read and why your arguments are so incoherent.

In science, "improbable" and "Impossible" are very different. Improbable means possible, but unlikely. Impossible means not possible.

For example, what is the probability of a mountain spontaneously teleporting to the opposite side of Earth? It's highly improbable, but not impossible. What is the probability of abiogenesis? It's highly improbable, but not impossible.

Please re-read all the posts and the papers again now that you know the difference. Hopefully you will be able to understand them now.
Vietvet
4 / 5 (4) Jun 18, 2014
@feath3r

If not abiogenesis, how did life arise?
animah
5 / 5 (3) Jun 18, 2014
Priceless!

I use words in their technical contexts, and you try to rebut me by quoting their everyday definitions.

I used "improbable" in 2 contexts that would be obvious to a practitioner.

There is "algebraic probability". In this case, the probability of life emerging. It is improbable (life is rare), but obviously not enough since it has happened at least once (see "no hidden variables").

Then there is "geometric probability". In this case, the probability that the geometry of physics allows it. It is probable, because all observed phenomena related to biology have always been shown to be natural (see "epistemology of science").

These expressions are formal concepts. I put them in quotes so you could Google them.

Then again I'm pretty sure they're on the High School curriculum these days...
animah
5 / 5 (3) Jun 19, 2014
"People think that epilepsy is divine simply because they don't have any idea what causes epilepsy. But I believe that someday we will understand what causes epilepsy, and at that moment, we will cease to believe that it's divine. And so it is with everything in the universe."

Hippocrates, fifth century BCE.

I've said my piece, which was to warn that this research is being misused by a small group of very vocal quacks against the authors' wishes (and in the case of Orgel, with sad disrespect for his memory).

Moving on :-)
feath3r
1 / 5 (4) Jun 19, 2014
But life is an observable phenomenon. It is therefore NOT improbable.

the probability of life emerging. It is improbable (life is rare)

animah,
You consistently contradict yourself and engage in an empty word game in an attempt to save the face at the expense of truth. You readily insult people out of pride and fear of losing. You need to do some soul searching and get help. Goodbye.

P.S.
Ask any physicist. Just because Big Bang "has happened at least once" does not make it probable - it is still a highly improbable event.

P.P.S.
How ironic you speak of Hippocrates. Here is how Hippocratic Oath starts:
"I swear by Apollo, the healer, Asclepius, Hygieia, and Panacea, and I take to witness all the gods, all the goddesses, to keep according to my ability and my judgment, the following Oath and agreement"
Icemoon
1 / 5 (2) Jun 19, 2014
Pressurised collapse of asteroidal material within an ultra saline solution.
nowhere
3.7 / 5 (3) Jun 20, 2014
Ask any physicist. Just because Big Bang "has happened at least once" does not make it probable - it is still a highly improbable event.

Not true. We have no understanding of the events or reality that resulted in our big bang, and so the probability of big bangs occurring is literally a question that is outside our universe, and therefore at this time undefined.

How ironic you speak of Hippocrates. Here is how Hippocratic Oath starts:

This is relevant because we all know a man's faults invalid his achievements. This is why we don't use Newton's laws, because he believed in God.
feath3r
1 / 5 (4) Jun 20, 2014
nowhere,
There have been a myriad of quantum vacuum fluctuations occurring everywhere in our universe for billions of years. The very fact that our universe has not been wiped out by another Big Bang indicates that the Big Bang is a highly improbable event.

The context of Hippocrates is not about his achievements; it's about his quote being used against divinity. Therefore Hippocratic Oath is very relevant because it shows that Hippocrates himself believed in the divinity.
endfraudnow
2 / 5 (4) Jun 24, 2014
Seems to me that being men of science, you would realize that life began when it was CREATED by God Almighty.
nowhere
5 / 5 (2) Jun 25, 2014
There have been a myriad of quantum vacuum fluctuations occurring everywhere in our universe for billions of years. The very fact that our universe has not been wiped out by another Big Bang indicates that the Big Bang is a highly improbable event.

AFAIK the BB did not occur within an already existing 4 dimensional universe, but was the origin of that universe. Why should future BB's then occur within our universe? If they do form, would they not be "next" to us rather than inside us?

The context of Hippocrates is not about his achievements; it's about his quote being used against divinity. Therefore Hippocratic Oath is very relevant because it shows that Hippocrates himself believed in the divinity.

Ad hominem fallacy. The quote is a valid statement. His beliefs do not change the validity of his statement, or even offer any valid reasoning in favour of divinity.
endfraudnow
1 / 5 (4) Jun 25, 2014
Since NO credible evidence has ever existed for one species turning into another in the fossil record, and the scriptures say that each creature was created in it's kind, and all evidence purporting to be such a transitional creature has all, and I repeat, ALL been shown to have been fraudulent, and the efforts of mankind to create things always mimics what God created, then the only logical (provided you're not a Bible studying person) conclusion is that it was created. It was in fact all created by God Almighty. The retarded viewpoint that there is some primordial soup from whence life originally came is completely without merit and shows a total disregard to the One you should worship righteously.
animah
5 / 5 (2) Jun 25, 2014
fossil record

A partial list of hundreds of transitional fossils:

http://en.wikiped..._fossils
-

you should worship

Off-topic and irrelevant.
feath3r
1 / 5 (3) Jun 25, 2014
If they do form, would they not be "next" to us rather than inside us?

nowhere,
Here is an article that talks about how an alternative universe can arise within ours via quantum fluctuations (according to Lykken at Fermi lab).

"An 'alternative universe' will eventually destroy ours, says Higgs researcher"
http://io9.com/59...searcher

P.S. It is your prerogative to continue to ignore the context of Hippocrates quote being used here.
animah
5 / 5 (2) Jun 25, 2014
shown to have been fraudulent

CITATION NEEDED
nowhere
5 / 5 (1) Jun 26, 2014
nowhere,
Here is an article that talks about how an alternative universe can arise within ours via quantum fluctuations

The article talks about how a new universe may form within an unstable universe (turns out ours may be unstable!), however for you to assume this is the primary method of universe formation and base probability off of it is ridiculous. Especially when you consider that they don't expect it to happen for many tens of billions of years from now.

P.S. It is your prerogative to continue to ignore the context of Hippocrates quote being used here.

I'm ignoring it because, in the context it is used, his belief neither challenges the quote nor futhers your argument. It is therefore irrelevant.
feath3r
1 / 5 (2) Jun 26, 2014
however for you to assume this is the primary method of universe formation and base probability off of it is ridiculous. Especially when you consider that they don't expect it to happen for many tens of billions of years from now.

nowhere,
Please study quantum fluctuation and statistics. The only reason they don't expect it for tens of billions of years from now is because, as I have already stated, the event is HIGHLY IMPROBABLE. It does NOT mean that there is some kind of guarantee the event would not occur until billions of years pass. If you know anything about probability, you'd know that it can happen at this very moment. But, due to its high improbability, a REALISTIC guess is the billions of years. Thus the article is basically repeating what I have said.

http://www.npr.or...universe
"Lykken tells us. "So in principle it could happen tomorrow"
nowhere
5 / 5 (1) Jun 27, 2014
feath3r,
Please study statistics and learn a bit about the BBT. Here let me fix your comment so that it is correct.
'The very fact that our universe has not been wiped out by another Big Bang indicates that [a] Big Bang [occurring within an already formed, borderline unstable, universe] is a highly improbable event.'

This however says nothing about the probability of BB's occurring in general.
feath3r
2 / 5 (4) Jun 27, 2014
nowhere,
First you falsely claim BB would not occur within our universe. Then you make another false claim that if BB does occur, then it would be "next" to ours. When I correct your false claims, you reveal your scientific ignorance by saying, "Especially when you consider that they don't expect it to happen for many tens of billions of years from now." So, I had to correct you on this, too.

You never acknowledge that you were wrong, and you continue to make a futile, unscientific argument. Again, it's your prerogative to believe whatever you want to believe. Goodbye.

P.S. Here is a hint - try explain how our universe was created without using the words "quantum fluctuation". Unless you are a creationist, good luck with that, because now you're arguing against modern physicists.
http://www.npr.or...erything
"universe came out of quantum nothingness,"
nowhere
5 / 5 (1) Jul 01, 2014
feath3r
First you falsely claim BB would not occur within our universe.

Straw man.

Then you make another false claim that if BB does occur, then it would be "next" to ours.

If all BBs form inside existing universes, where did the first one form?

When I correct your false claims, you reveal your scientific ignorance by saying, "Especially when you consider that they don't expect it to happen for many tens of billions of years from now." So, I had to correct you on this, too.

Incorrect. I thought you were referring to the theory as improbable not the event. Since there was a miscommunication I returned to your original incorrect statement.

You never acknowledge that you were wrong, and you continue to make a futile, unscientific argument. Again, it's your prerogative to believe whatever you want to believe. Goodbye.

I corrected your statement, the original point of our debate. Rather than address it you rely on a straw man argument to avoid it.