My name is LUCA

MyNameIsLuca My name is Luca, I’m your last universal common ancestor .. and I don’t exist.
I’ve come to tell you that you don’t exist either, not like you think you do.
I know this, because a very long time ago, I was you!
    
        Let’s start at the very beginning. With all the discussion going on about ‘Evolution’ and the inclusion of its antithesis ‘creationism’ in the school-curricula of southern states of the U.S.A., one may be excused to think more of this discussion will follow here. However ‘Evolution’ is not the issue at hand and it is rather surprising that it is the issue at hand anywhere. As a scientific theory few others can claim to be as complete and as supported by evidence as this body of knowledge is. Today we will discuss another part of biology, where we unfortunately still speak of multiple hypotheses and about research that is continuously updated. It is not a particularly easy subject and therefore not part of the any common high-school curriculum.  It also doesn’t feature such visually insulting pictures as ancestor-apes. But it does not contradict the religious genesis story any less than Evolution theory and, in fact, it does it on a more fundamental level. A reason for ‘theist-silence’ on this matter may be that many of them confuse it with the actual theory of Evolution. The often ignorant comments on articles supporting evolution do suggest this. Now, let’s talk about abiogenesis.

        Abiogenesis is the biological study and developing theory about how life can and did originate from non-living matter. It is a particularly interesting field of study because it has implications that take it from missions to Mars to computer science and the study of artificial intelligence. But more than that it has the power to change how we think about life as a concept and about ourselves in particular. There is something about the way abiogenesis tries to explain how living cells came about that flies in the face of even the most rational human. Our ‘Sensation of internal complexity’; our sensations of “Self” contradict with any such mundane and simple beginning. Even a cursory detached review of all the features of the human body seems to suggest an asymmetrical design process. The mind, with its self-awareness and its awareness of the rest of the body does not allow for the imagination to reduce itself to mere rearrangements of ‘stuff’. The very idea that a living thing is produced with non living components implies intuitively that:
    1)    There once was a time without life
    2)    The transition between alive and not-living is not discrete.
    3)    Therefore any living thing must necessarily be considered alive only to a degree of coherence with a definition. The definition of what is alive being an agreement and not so much an intrinsic property which needs only be detected.

For your entire life you have thought you were you, but you are not. You are a multi-cellular organism of the eukaryote domain. Your are an ‘organism’,  as in ‘organization’; A unit composed of cooperating sub-units, derived from the ancient Greek word for “instrument, tool”.

You are a blob of cells, and we are not able to draw a neat distinction between a ‘blob of cells’, a ‘colony of cell’ and a single multi-cellular organism. Likewise we have not drawn such clear distinction between things that ‘live’ and thing that do not. We say we ‘kill’ viruses. We talk about a virus being ‘dead’ inside a body or ‘extinct’ inside a population. We talk about a virus invading our cells and mutating or evolving to ‘counter’ antibodies. But a virus is just a collection of atoms, formed into long chains of molecules. A virus does not have the capacity to show intend. A virus cannot reproduce and it does not eat. By all but the most permissive of definitions a virus is not a living thing. And yet, like a virus, you are just an arrangement of atoms. A lot of your DNA has viral origins. For the most part these genomes are non-functional, for the other they’re beneficial. As a eukaryote you have organelles inside each of your cells which are basically proto-ancestors of bacteria (endosymbionts) with which you formed a mutually beneficial relation. These still carry much of their own DNA and broadly speaking these organelles are individually more alive than the flew-virus ‘you just overcame’.

Now what is this thing we call ‘being alive’? As suggested there is more than one definition, but most include something along these lines: “Living organisms are systems with self sustaining biological processes which can replicate imperfectly.” One biological process involved is a metabolism, a way of converting material sources to biological components using some source of energy.  Growth, as a consequence of that metabolism is also often mentioned in definitions. The central part however is having a build-in way of self-replicating. However, in reproduction, perfectionism is not the way to go. Imperfect reproduction causes better adapted offspring at the cost of the demise of the less adapted.

 As a blob we call ‘human’ we expect you to sleep about 8 hours, be active for 16 hours out of 24 every day and that for the coming 78 years. After that you will probably be a blob no longer. During all this time you will rather consistently show most of the characteristics of a living thing. Not everything plays as nice as you though. Not everything is as alive as you are all the time. Take for instance a plant-seed? Should we consider that alive? The Cicada is an insect that arises (with its siblings) from the ground interspaced by periods of up to 17 years. Should we consider them alive during the stage of diapauses? In most rocks, like basalt, bacterial life can be found. Some of the bacteria found at extreme dept hardly have any metabolism at all. They reproduce by cell-division once in a millennium. Are they alive in the hundreds of years they are just as still as the basalt molecules that surround them?

Life founded in iteration

Life is an emergent phenomenon. ‘Emergence’ is a term we coined for non-trivial patterns that arise from the interaction of simple agents. In the simplest of examples an ocean-wave is an emergent phenomenon, a collaboration of water molecules and energy. As it stands earth-life is a collaboration of organic molecules. All emergent phenomena share the characteristic of iterative processes in which order is begotten out of chaos.
A well known example of a spontaneously iterating process is the Belousov–Zhabotinsky reaction. This was a chemical experiment in 1958 which unintended results at first defied believe. This was one of the earliest discoveries of non-linear chaotic systems. This reaction, which can be done by anyone, involves an 18 stages color-cycle which repeats over and over again.  It serves us to demonstrate that chemicals can run, like engines (ex.: Stirling Engine), and go repeatedly through the same processes, depending only on the input of energy.

Belousov-Zhabotinsky
http://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Bzr_fotos.jpg/220px-Bzr_fotos.jpg

To be clear, it is not a question whether life as we know it can be made from simple chemical interactions. Self-sustaining iterative chemical reactions that make imperfect copies of themselves might not be trivial to make, it is certainly not beyond the ability of many of the bio-chemists that study abiogenesis. Whether those molecules would also evolve into intelligent or even organized life only a billion years of time could tell. It is not so much the question whether a bio-chemical system with the properties of living things can be formed, the question is how and under what circumstances did this spontaneously happen complying  with all the things we know about early-earthian environmental conditions. Critics of abiogenesis as a principle often play the ‘chance’ card. For all components of a minimalistic living cell to come together by chance at the same time and place; they state, would form an infinitely small probability. Usually numbers are quoted, which cannot be exact by any means since this would assume intimate knowledge of the early-earthian circumstances. Besides, these critics entirely miss the point of abiogenetic theory up to now: that the first living cell was gradually grown from non-living but functional chemical precursors rather than begotten at the throw of some very lucky dice. On top of this it must be clear that, while many of the processes described in abiogenetics are driven by small probabilities, the geological time during which they took place multiplied by the vast theatre in which they could act more than makes up for this. In fact we have indirect evidence that life came about almost as soon as geological conditions would allow for it to exist. Al together it might in fact only have taken a couple of million years. Yes, I agree, ridiculously fast!

You might be wondering, if abiogenesis was so easy why then didn’t we see it happen over and over again in the last million years. The short answer is that the descendants of LUCA have literally invaded every nook and cranny of this earth and greedily incorporated the largest part of the resources that abiogenesis would rely on. The complicated answer is that the abiogenesis of LUCA was probably not such a linear process but likely absorbed several independent spontaneous processes to make a patchwork of a first living cell. Think about the fact that we have not 1 but 2 knowledge-carriers in our cells, RNA and DNA.

 To understand how chemical processes may spontaneously make up functional parts of a living cell one must first realize how chemical substances are ‘pre-programmed’ for certain natural actions. The basic unit of chemistry, including biochemistry, is the atom. Atoms have one or more layers of electrons swirling around them which are bound to the atom by the electro-magnetic-force. Each atom has a specific weight and has a number of electrons in its outer layer. These factors determine the nature, the strength and the preference with which atoms will bind with each other. Globed-together atoms are called ‘molecules’. These have binding-preferences of their own depending on the atoms from which they are made. Bindings most often take energy to form, decoupling as a rule produces energy. Bindings of a molecule influence each other, weakening or tightening with subsequent bindings.  Finally, it is important that you understand the workings of the catalyst. This is a molecule which temporarily binds to two other substances which, as a result, find it easier to bind with each other. After this last binding they both release the catalyst in its original state ready to enable the same reaction again. It is probably the centerpiece of organic-chemistry.

Catalysis
http://en.citizendium.org/images/8/81/Catalysis.png

We can identify several factors that are important in any reaction and certainly so in biochemistry:
    •    Proximity of substances/resources.
    •    Concentration of substances/resources.
    •    Absence of other competing reagents or other inhibitors.
    •    Presence of an energy source.
    •    Limited amount of energy.

The hypotheses

There is no space to at length discuss the different ideas and evolutions that occurred in abiogenesis. A fairly comprehensive text can be found here. For those with less appetite I will derive some core lessons.

The first thing we must concede is that, while we have made considerable headway into explaining how life on earth came to existence there is currently not one hypothesis which is exhaustive enough or supported enough by experimental evidence to be subscribed to by a majority of biochemists. One of the most hindering factors is absence of a complete and stabile description of early-earthian circumstances. Whenever any adjustment is made in this model this automatically impacts the chemistry that would have been plausible. As a whole we can say that every hypothesis has its problems. These problems may be analogues with problems many of us face in our day-planning-schedule. Some hypotheses are in Paris while they have a meeting in New York in half an hour. These hypotheses are interesting but a solution to them is unlikely to come easily. Other hypotheses merely face a conflict between ‘picking up the kids’ and ‘passing by mom’s’. If we can get mom to ‘pick up the kids’ we can pass by her place later and have it both ways. Like this several hypothetical models may eventually help to solve each other’s problems.

The split

While they are not mutually exclusive the abiogenetic world is largely split into two different approaches to cell-mechanics. On the on hand there is the ‘metabolism first’ approach, on the other hand we have the ‘genetic reproduction first’. Both ideas claim that their process is more likely to have been first and to have caused the other. It is however quite possible that both developed parallel to each other and that there were dialectic, mutually beneficial, influences.
In the metabolism-first approach researchers focus on chemically stabile iterative processes like the citric acid cycle and the reverse citric acid cycle. The latter being a part of several spontaneous metabolism experiments. One of these hypotheses centers on the volcanic hydrothermal vents below the oceans. In summary, experimental setups which duplicate specific circumstances, have proven that in very little time all necessary amino acids, sugars, bases and larger organic molecules do in fact spontaneously generate. The exact correct circumstances still being somewhat of a question the continuing research will focus on whatever seems likeliest next. While this in itself is nothing less than astonishing, basic problems still exist: how to explain the formation of the larger molecules to explain genetic reproduction, how to explain how all resources were sufficiently concentrated as to make these reactions possible, explain how the reagents were sufficiently shielded from inhibiting reagents as to make the reactions possible.
The most famous experiment in this context is the Urey-Miller ‘primal soup’ experiment in which the synthesis of biochemical molecules was first demonstrated. While the premises to this experiment have since been severely revised the conclusions were upheld by other sort like experiments. No-one however claims that they demonstrate End-to-End how life came into existence. By itself it is not sufficient to prove a spontaneous generation of life. But is in certain that Urey-Miller -type processes synthesized molecules that were used by other mechanisms to construct stabile protobionts. While several problems remain for these first hypotheses, simultaneously solutions to them have been proposed and some even demonstrated to work.

Urey-Miller experiment http://www.biologycorner.com/resources/Miller-Urey_experiment_wiki.png

Factors of synthesis

Several factors have stimulated the formation of larger molecular chains necessary for life. Minerals for example play an important role in many metabolism-first hypotheses. They act as catalysts, provide the chemical-energy necessary for the metabolic cycles. They provide protection against UV-light and would have made up most of the rock-formations that both protected tidal pools from the waves while allowing them to concentrate through evaporation and so enhancing the possibility of reactions taking place. Mineral surfaces on seafloors may have locked sedimentary chemicals into place until other reagents arrived, working both as a catalyst, a mold for molecule structuring and a concentrator.
Crystals are another element that, through letting substances of certain size inside, would have acted both as a concentrator and a protective enclosure for reactions to occur. During experiments it was demonstrated that the sugar phosphate backbones of our DNA, RNA  and of ATP could spontaneously form inside certain crystals given the presence of the right elements.
The process of gradual crystallization of molten (volcanic) rock is another process which has tremendous potential for concentrating necessary components. Long polymer chains are automatically composed during the solidification phase. While these would at first be locked inside the rock, erosion would have released them as a steady source of compound molecules. Given the massive amount of rock the earth produced this is a factor of significant importance.
Space is another place where chemicals can gradually build up to bigger and bigger molecules which then rain down and provide ‘food’ for autonomous chemical cycli. Space nebulae contain large quantities of hydrogen, nitrate, and oxygen. Spectral analysis also indicates that they contain large quantities of organic molecules (140 identified). Space has the advantage of freezing dust together and periodically heating it up with UV-radiation to reaction temperature; thus acting both as a concentrator and an energy supplier. The supply of monomers (chains of molecules), lipids for example, from space has been attested to. Space is also mentioned in regards to the ‘panspermia’ hypothesis that states that life needn’t have synthesized on earth and could quite easily have been collided off of other planetary bodies. This hypothesis is not without merit as it would significantly enlarge the theater in which life could have arisen, but it also makes it a little harder to pin down the exact circumstances abiogenesis actually dealt with.
In summary there are ample sources for monomerical building blocks. The true challenge lays in filtering out the right building-blocks and assembling them in bigger entities. Life today only uses a handful of building-blocks, mostly carbon based,  and a comprehensive metabolism theory should account for this.

In the formation of larger organic polymers something as simple and readily available as clay may have played a significant role. Clays consist of nutrient rich layered structures  (1 tetrahydral layer followed by 1 octahedral). Sometimes these are formed in 3-sequential patterns. Between the layers molecules can be trapped and subsequently caused to react. Clay usually also has an electric charge with which they can attract chemicals and bond with them. Clay has therefore been proposed as a possible scaffold for RNA. A problem that might arise is that large polymers would have trouble to separate from its scaffold. This would predict that in the so assembled molecules clay-residue should be found. In experimental setups mall RNA strands were actually synthesized, with small clay-residues still imbedded into them. Though impressive, the latter test must be seen as a prove off concept only.

Cell membranes

Another problem we talked about was the need to separate reagents from other non-useful reagents and containing them so as to permit the right reactions taking place. A protective membrane would do the trick but would have to come about without the benefit of being synthesized as there would be nothing around complex enough to synthesize it. A simple example of such a membrane is a double layered lipid structure. Water and lipids don’t mix but when a phosphate group is attached lipids ‘like’ water again. The resulting structure is polarized with a side that likes water and a side that doesn’t. Such polarized molecules cling together into ‘sheets’, into the state of least energy, where the hydrophobic ends join to ‘protect’ each other from the water. Two sheets of lipid-phosphates in water will layer with the hydrophobic sides close together. With enough molecules these double layered sheets curl into a sphere because a sphere is the structure with the least required energy and at which this bunch of lipids is the most stabile. They thus inclose a body of water in which any collection of chemicals is more protected then before.  Lipids from egg-yolk spontaneously form spheres when they are inserted into water. These spheres are called vesicles (there is also a single layered version called ‘micelle’). The amazing thing about these vesicles is that they immediately allow for a primitive form of darwinistic selection. A vesicle packed in close with other vesicles will expand due to internal pressures when it harbors a successful molecule-producing process. By pressing the vesicles around it it will absorb the lipid-phosphates from neighboring vesicles (that eventually seize to exist). This process was experimentally verified and provides a significant selection advantage to successful iterative biochemical processes.

Vesicle and mycelle
http://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Phospholipids_aqueous_solution_structures.svg/180px-Phospholipids_aqueous_solution_structures.svg.png

Self-replication

The big difference between a metabolic process and a genetic one is that a metabolic process may synthesize any molecule while a genetic process needs to makes copies of itself. Metabolic iterative processes may be smaller and easier to spontaneously combine, the second instance of them is every bit as hard to make as the first.  A genetic molecule (molecule chain) on the other hand may be quite a lot larger and much more difficult to generate, as it contains information about how to make itself, the cost is entirely borne by the very first one. Once a genetic process has been established it can allow for variations in its replication.  This can lead to other replicators or larger, more complex metabolic processes.
Modern genetics replicates as well as, with subsections, synthesize molds(RNA) that in turn help construct all parts of the organism. However it is quite certain the earliest self-reproducing molecules did not encode for other metabolic processes. Contrary to current genetics they probably didn’t need more than a vesicle and a steady influx of resources to bind with until a copy was made and released. The early genetic molecules are thought to have been autocatalytic. This avoids the remote chance of genetic-chains and the necessary catalysts spontaneously forming at the same time and place. Modern DNA however is not autocatalystic and relies on complex proteins for catalyzing the reproduction reactions. Explaining this difference is a challenge to the ‘genetics-first abiogenetics’. An attractive variation on reproduction may also have existed in the case of early genetics. This is cross-catalysis. A metabolic-molecule A makes a metabolic-molecule B which in turn makes more of molecule A. This also illustrates how a cross could have been made from a purely metabolic process to a genetic one. An experimental ‘proof of concept’ of a self-replicating genetic chain was made with a genetic molecule consisting of adenine, naptaline and immite. While an example of a primitive self-replicating molecule this is not considered a viable candidate for the actual genetic precursor.


The RNA world

The most influential ‘genetics-first’ theory revolves around the formation of RNA and RNA precursors. An important reason for this is because it was discovered that RNA not only encodes for the genetic information but, when spontaneously folded up into a ball-like structure it can act as a catalyst for its own replication. Experimental tests on spontaneous RNA creation were successful. With RNA pre-cursors hiding in lipid vesicles there also was no hypothetical need for membrane synthesis or any other type of metabolism. Yet, while it seems this theory has everything it needs end-to-end, there are several problems still. Despite the experiments RNA is still a large molecule to form. There is no explanation how RNA could lead to a metabolic process. Furthermore there are indications that metabolism did in fact precede RNA. Taking this into account RNA is quite certainly an important phase in any transition form metabolism to DNA. Alternative experiments have had rather a lot of success replacing the sugar backbone of RNA with, for instance, glycerol thus making GNA. This is an altogether more easily generated molecule which supports the higher temperatures of the deep earth and near the volcanic hydrothermal vents.

DNA strand

http://www.biologycorner.com/resources/DNA-colored.gif

Extremophiles

In the last decade technological advances have led to discoveries of life in places that were once thought uninhabitable. This has had great influence in our thinking on abiogenetics and proposed solutions to problems the hypotheses were faced with. Simultaneously the hope of finding live on the unwelcoming plains of rough planets like Mars increased. Whether or not life did have a extraterrestrial origin will only be confirmed if we find something there, and specifically on what we actually find. In all the research into extremophiles has pushed the envelope for the basic assumptions beneath abiogenetics.

Conclusions on abiogenetics

There exist roughly three views on the likely path of atom to living cell:
    1.    Life began autotrophic, starting with metabolism, only latter incorporating genetic molecules in the mix.
    2.    Life began with genetics, possibly autotrophic possibly heterotrophic. Metabolism came with more enriched genetics.
    3.    Life was a cooperation of a genetic system and a metabolic system.
None of these paths is complete in the sense that they provide us with a supported end-to-end story on how atoms arranged themselves into subsequent phases to form LUCA’s ancestor. Three questions await a definitive answer:
    •    The origin of biological monomers.
    •    The origin of biological polymers.
    •    The evolution from molecule to cell.

For all partial explanations have been provided. Monomers can be synthesized in the primordial soup, near deep sea vents, inside the rock-formations in the crust, in mud puddles and in outer space. Cell membranes clearly self-organize by way of lipid-phosphate vesicles. Self-replicating molecules are possible in lab-conditions and several hypotheses exist for either RNA, an RNA precursor or a self-reproducing metabolic cycle to have been the original replicator. Certainly RNA once was the dominant biomolecule on the planet only to lose its role once protein catalysts and more efficient DNA chains had formed, reducing RNA to a messenger molecule.
 

The 747 gambit

Theists enthusiastically compare evolution (and the abiogenetics they don’t distinguish from it) with a scrapyard being visited by a twister, leaving an entire 747 as a finished product. Since this seems rather an unlikely event they propose life and that 747 must have had a supernatural cause. Remaining in the same metaphor we can adjust this image however. It is not so much a 747 being blown together as well as an endless line of little plastic planes being 3D-printed; with, after every batch, a floating test to decide what printer may produce the next generation. The assembly of the end product only happening due to purely natural processes in suited environments with different ‘platforms of stability’ for different parts, working for millennia and millennia and mill…
Once one of the planes is able to support itself and to reproduce independently the 3D printing becomes obsolete. Little planes take over the world, compete, grow and evolve. Millions of years later a 747 takes of from JFK. Remember, it’s just a metaphor.
While the end-to-end theory is not out just yet, there is enough that indicates that the natural cause was what actually happened. Let’s begin with the modular way in which living things are build out of different quantities of the same building block, the single cell. Why are there so few unique parts that would attest to the complex design? Think about the shape this single cell has, being the least costly structure and the only one we know that forms by itself, a globe. A cube-shaped cell would make more sense in a design-process, think about it, you would be able to stack pigs in the cargo-space of a ship if this were the case. Another weird thing, for a designed object, is the happenstance build-up of that cell. Mitochondrial DNA, nuclear DNA, three types of RNA which has catalytic functions it doesn’t even use anymore. Why do we need viral DNA in our DNA? And why, for the most part, does it just sit there?
Abiogenetics is an unfinished race. Creationists are still at the starting line yelling how science will never get there, how it is even running in the wrong direction. Science has seen too much along the way tough, things creationists refuse to acknowledge, for it to stop and give up. Besides science is only getting warmed up and pretty soon abiogenetics will see the finish-line. It may never actually cross it until life is discovered on Mars, but the yelling of the creationists will go the way of the ‘flat-earth-theorists’; it will grow very, very faint.

My name is LUCA, I don’t exist anymore and what I was no-one will ever find out.
But you know I existed. So think of me with all the descendants of me that are in you.
Think, and I will be! Think, therefore I am!

The Silent Atheist

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