Jens

 

http://sws.bu.edu/msoren/Carstens.pdf

http://mbe.oxfordjournals.org/content/25/2/402.short

http://genome.cshlp.org/content/22/4/746.short

 

I will read to the three of your distinct links which are public. I Just need some time for it.

(...and will try to adapt to the technical language used for better understanding between us....)

Try this video

 

The video provided is fine for schools (if you stay at that high level).

It also explains in a good way the current status of know-how to non-scientists and addresses in a simple way a lot of "critics" raised by religous fundementalists and I wish you all the best with the battle against creationists (I like your statement "You do not possess belief, belief possesses you...").

 

But this is not a discussion in this topic.

 

My topic here addresses scientists or people with good biochemical understanding (final university level). Your video rightly stated "It has to be said that this research is in its infancy and current hypothesis are no where near as solid as the theory of evolution..." I am drilling into these details here and my proposal is much further than the video.

 

By the way:

- The chemical formulars in the video contain some errors (at 0:33, 1:38, 2:17)

- RNA does not attract the hydrophopic part of membrane lipids. RNA is completely hydrophilic and cannot bind to the hydrophobic part of a membrane lipid as shown in the video. The shown cell does not work.

- The video seems to imply the order RNA -> DNA -> Protein, which no scientist is claiming. In fact the only open debate is about if RNA replication and protein biosynthesis evolved jointly and initially or one after the other. DNA is nothing more like a tape storing information which was introduced rather late in origin of life (and surely after protein biosynthesis).

- The video stated "One of the differences of RNA and DNA is that DNA needs proteins to replicate itself" and implies further that this is the main reason why protein is needed. Sorry but that is completely misleading (or to put it frankly: simply wrong). Today both RNA and DNA need proteins to replicate. The main difference between RNA and DNA is that RNA can act as an active catalyst and DNA not (discovery of this was a nobel price, if I emember correctly). This is because RNA (unlike DNA) can form precise and nearly arbitrary three-dimensional structures (depending on its sequence of bases). So the obvious speculation is in the past RNA could be replicating itself (which DNA could never do). ...and this is not my personal view but simply the current status of discussions in the scientific community....

 

I am willing to help to improve such videos in detail (if you know the authors, of course I would help to change it to the current main stream opinion in science and not to my personal one which I present here). It is nevertheless a good video.

 

Just another example: The whole basic sense (let alone the more advanced features like electrochemical gradients) of a membrane is to keep the concentration of water soluble intermediates inside the cell different than outside (in order to allow longer chemical pathways e.g. for synthesis of the biomolecules or to activate the nucleotids to replicate RNA). However, if a membrane is able to do this, nothing from the outside can enter any more, especially the highly polar molecules the RNA is made of. And even worse: RNA is completely incabable to create hydrophobic surfaces needed for transmembrane carriers. You need protein for it. This means most likely evolution already started before first membranes where established (since otherwise you have to assume that a complete cell with RNA, primitive ribosomes, primitive adapters, tons of enzymes, carrier proteins and a membrane sponteneously was formed, which is nonsense. Or you find better other alternatives like Wächtershäuser's theory).

Lets back this up just a small amount, there are other schools of thought about the origin of life. I've skimmed through your links and while I cannot critique them I do know that they are not the last word.

Of course I am not claiming to have the last word. However, a self-replicating molecule first (RNA or something similar to it) is still what the majority of scientists currently prefer above the low molecular chemical cycle first (metabolism first) school of thoughts. This is no argument of course, but should be known as context of the discussion: see e.g. RNA worlds.

I don't understand this statement, when you have an entire planet full of various chemical cycles going on continuously with no doubt billions of reactions a second even the improbable becomes inevitable and RNA needn't be the first self replicating molecule.

What is stated by Wächtershäuser is that there was a stable "autocatalytic" cycle of low molecular substances (in a stable steady state environment like in current deep sea black smokers) and not a random chaotic environment. There is a claim by Wächtershäuser that this chemical cycle slowly evolves into more complexity. Note that this cycle is autotrophic (independent from organic molecules) right from the beginning. Orgel (after supporting this theory initially) shows the mentioned severe issues with this.

 

There is no detailed theory of how life could start with chemical cycles (and without self-replicating large catalytic molecules) in a chaotic (unstable) environment. If you know one, please provide a link.

 

I agree that RNA does not need to be first molecule. But I agree with the current majority that a self replicating macromolecule able to do catalysis was in the beginning and not a metabolic cycle of multiple low molecular substances.

 

I will answer to the rest of your post also (just have to leave now)...

Thanks for your input and discussion!

It's still highly unclear what you're trying to do - it seems you're trying to resolve deep nodes in a tree of highly divergent organsims, but from your figures, it appears you're constructing a phylogentic tree from paralogous sequences.

 

This fundamentally violates many assumptions underlying any of the tree building methods used.

I fully agree. But this is what have been done and have been claimed in PNAS by the following paper:

http://www.pnas.org/content/102/52/19003.full.pdf+html

The Evolutionary Relationship Between PheRS and SepRS. Our analysis further demonstrates that SepRS and the associated indirect aminoacylation pathway for tRNACys are truly ancient, already present at the time of the LUCAS.

And the same in a similar case for pyrrolysine. In other papers this wrong conclusion is than used as argument of how the genetic code evolved (This is how I came to the topic.)

So you confirm my assumption that the conclusion by O'Donoghue cannot be drawn, since they constructed a phylogenetic tree out of paralogous sequences and draw conclusions about the time of branching. This was my main target.

B) If you're trying to construct a tree representative of whole organismal diversity

This is not what I try to do.

 

Side Question: Is from your point of view the following statement right:

If a phylogenetic tree containing a mixture of homologs and paralogs is constructed (even though you should not do it ), the branching point of the paralogs is biased in a way that it appears to be earlier than it actually was (but not later). This is especially true for very ancient trees.

I probably better post chapter VI completely here to explain the method point:

 

Figure 1: Evolution of paralogous proteins in different species. The different paralogous proteins are indicated as A, B and Z. The different species are indicated by different color (black, blue, magenta and green). Time flows from bottom to top. Horizontal distance means distance in similarity. Protein A and B are functionally closely related, protein Z is functionally more distant. The filled black circle B indicates the point in time in which a copy from A was created and evolved into closely related function B. The filled blue circle Z indicates the point in time in which a copy from A was created and evolved into more distant function Z. The open colored circles indicate the origin of the respective species. Lines are going back and forth horizontally to indicate the more or less random sequence changes in the non-conserved areas of the protein.

 

Figure 2. Predicted functional tree versus actual evolution. Taken the exact same situation as in Figure 1 the assumption is that all non-conserved regions are fully randomized by mutations back and forth and that all the sequence of all conserved regions are fully determined by selection pressure (and do also not contain any historical information any more). The orange tree shows what every tree calculation method will produce. Even though there is zero phylo­genetic information left, still a tree with high confident branching points will be predicted. However, the tree only shows the functional relationship and will always predict any branching of paralogous proteins before LUCA, no matter what actually happened. Note that the order of time points of branching of B and Z is predicted completely wrong by the orange tree and that the sequence between branching of Z and the occurrence of the different species is also predicted completely wrong.

 

Figure 3 : Selection-driven tree versus mutation-driven tree. In orange the same 100% selection-driven tree is shown as in Figure 2. The black tree shows a 100% mutation-driven tree which indicates how the tree looks if all the phylogenetic information is still left. However this only works perfectly, if only the non-functional regions (which face random surviving mutations) are taken into account and the time scale is short, so that mutations back to the same sequence can be ignored. In all other cases you will obtain a tree which represents a combination of both trees.

 

Explanation in detail:

Phylogenetic tree prediction methods have to assume that differences in sequence occur random, since they are simply using mathematics and ignore biological function. They also have to assume that the amount of multiple mutations within the same branch at the same site can be ignored, since they do not leave any trace in the existing data (at least unless the number of surviving species used as input is much higher than the average number of mutations per site). The first assumption means that phylogenetic tree prediction methods assume that evolution only consists of mutation and ignore selection. The first assumption is false for proteins which share the same origin but do not share the same functions any more (paralogous proteins). The second assumption is false for proteins which appeared in the early diversification of Archaea, Bacteria and Eukarya or even older. If proteins are ancient enough all the sites which are not under high functional selection pressure get randomized by many mutations forward and back, so that you cannot trace the sequence of mutations and hence the actual evolutional relation out of the current sequences any more (see Figure 1). In contrast the sites which are under high functional selection pressure still stay related. This might be enough for homologous proteins (those who share origin and function) to still see rests of a phylogenetic relationship in those conserved areas. However, for paralogous proteins those sites differ systematically because of the different functional selection pressure. In the given example (see chapter Details I) this means that a copy of Phe-tRNA^Phe synthetase changed the function and adopted to bind Pyl instead of Phe and to bind the tRNA^Pyl instead of the tRNA^Phe. This means, if paralogous proteins are old enough (e.g. at the point in time of origin of methanogenic Archaea) you risk to obtain no mutation-driven phylogenetic tree any more but a selection-driven functional relationship tree (see Figure 2). This also explains the apparent paradox why it seems possible to obtain clear and highly resolved phylogenetic information about an event “clearly” before LUCA, even though the much more recent events of species forming within Archaea, Bacteria and Eukarya are often harder to resolve.

 

Of course the bias only works in direction to show paralog branching points systematically deeper than they are (see Figure 3) and never to show them to be more recent. So it is possible to deduct out of calculated trees that a paralog appeared more recently than a species branching point, but not the inverse. Even trees of homologous proteins might be biased, because of hidden functional differences like binding to different other proteins or RNAs or binding to different regulatory molecules because of different metabolism. True homologous proteins do not only share the main biological function but also need to share the same regulatory features (which are very often not known or verified).

 

To obtain trees which are more phylogenetic and less functional you should at least take all the > 95% conserved amino acids in the paralog out of the comparison, since they are functional driven and only compare the rest. If the branching point moves up in the tree in the reduced set, this is a strong hint that the tree with the complete data set was functionally biased in a severe way. If the reduced set is showing much more random behavior (e.g. species tree does fit much less to the canonical tree than the complete set), this is a hint that actually there is only very little phylogenetic information left and only high-conserved regions mutated slow enough to be still traceable. However, but exactly those regions are functionally biased. This means it is impossible to deduct any phylogenetic information about the paralog in this case.

I just read the topic and want to ask if your question or discussion is concentrated on the topic that existence of life on any other planet or existence of life without oxygen is possible or not

 

Existence of life without oxygen is possible. Life started on earth without oxygen and there are still today many Bacteria and especially Archaea which live under oxygen-free environment. Photosynthesis made it possible to take electrons from water (and thereby producing oxygen) to reduce CO₂ for production of biomolecules. So photosynthesis reduced the dependency of life from its environment dramatically (since light, water and CO2 are easy available) but definitely is not the first step of life. It evolved actually much later. It is a very complex "invention" by cyanobacteria which happened only once on earth and then was brought into some Eukaryotes (the plants) by using cyanobacteria a cell organelles (the chloroplasts). So life produced oxygen and not the inverse.

 

Thomas Gold speculated, somewhat controversially, that life is a naturally occurring chemical process that all nearly all planets develop at some point but generally becomes extinct as chemical processes change as the planet changes.

 

Hi,

as written above I like to discuss this in the other topic in this forum:

http://www.scienceforums.net/topic/71735-early-life-life-could-only-originate-early-or-not-at-all/

I have posted my answer and comments there.

thanks, Jens

I copied Moontanman's comment from the other topic because it belongs to this topic:

Thomas Gold speculated, somewhat controversially, that life is a naturally occurring chemical process that all nearly all planets develop at some point but generally becomes extinct as chemical processes change as the planet changes.

The real theory about life started as chemical process is coming from Wächtershäuser.
(you pointed me to Thomas Gold already, but there was not much content. However, if you like we can start the debate again.)
For example: Wächtershäuser G (1994) Life in a ligand sphere. Proc Natl Acad Sci U S A 91: 4283-4287. http://www.pnas.org/content/91/10/4283.short

Some argumentation against it is from L. Orgel who changed his mind at the end of his life (actually I found this very honorable. We have too little scientists who are willing to change their mind):
Orgel LE (2008) The Implausibility of Metabolic Cycles on the Prebiotic Earth. PLoS Biol 6(1): e.18
doi:10.1371/journal.pbio.0060018

Here my reasoning against autotrophic origin of life (for full reading see the pdf Early life what you see here is from chapter details IV page 11)

There are multiple issues with the autotrophic origin of life as proposed by Wächtershäuser:

• The unfavorable thermodynamics of polymer formation in a diluted environment as discussed above.
• One has already brought up by de Duve and Miller [43]: Any environment which allows for spontaneous polymerization near chemical equilibrium will simply randomize any sequence information (and kill life). RNA molecules with randomized sequence cannot be the start of life and further evolution.
• But main issue with Wächtershäuser’s theory is that autocatalytic small molecules cannot evolve. Life begins where molecule or set of molecules is capable of making a copy of itself and can undergo changes to evolve. If the active catalyst does not change, the produced molecules will not change. But in the proposed theory the active catalyst is the pyrite surface and not the ‘auto-catalytic’ small molecule which is part of a metabolic cycle. This means after a very short time the system produces all the possible molecules and will not change any more. Of course, if the small input molecule change, the same pyrite surface catalyst can actually produce different output molecules. However, since the active catalyst does not change, the chemical reaction always stays the same and will not evolve. The whole system will reach the maximum of complexity very quick and not evolve further. To start evolution (and life) you need a system in which the active catalyst makes an error prone copy of itself and hence has the possibility to reach different three-dimensional forms and gain other catalytic capabilities. Only exact three-dimensional folding allows stabilizing unfavorable intermediate states to allow for specific catalysis. To overcome this issue Wächtershäuser has introduced the concept of ligand feedback [40]. This concept postulates that some of the produced small substances bind to the surface as ligands and change the catalytic behavior of the pyrite surface, which in turn produces more complex metabolic cycles and more complex ligands. However, also with this assumption there is a fundamental issue: The ligand will win which bind strongest no matter which autocatalytic features it has. And this can and will happen at any point in time of the supposed evolution of the pilot metabolism. This is especially true in an environment with constant flow of water (as the assumed environment in Wächtershäuser’s theory). An autotrophic metabolic cycle in a constant flow environment will not evolve to biological complexity but rather will quickly reach a local optimum and not evolve further (if there is any evolution at all).
• Another issue is that the theory assumes initial evolution of life at very high temperatures. To overcome this there was the assumption that initially there is another form of macro­molecules which is more stable than RNA at high temperature. If there is really a form of “RNA” which is more stable in heat and simpler than usual RNA and if life really originated in hyperthermophilic environment, why are modern hyperthermophilic organisms not using it anymore? In addition there are some special adaptations to heat especially the higher GC content and reverse gyrase [44] which also indicate that hyperthermophily is not the default environment of life. In contrast to usual topoisomerase I which is just relaxing negative supercoils (without consuming ATP) caused by unwinding of the DNA during replication, reverse gyrase is actively (by consuming ATP) introducing positive supercoils into DNA to prevent unwinding of DNA at high temperatures. It is present both in hyperthermophilic Archaea and hyperthermophilic Bacteria. If life really originated in an hyperthermophilic environment, instead of changing GC content from the statistical distribution you rather expect an original set of the bases which all form 3 hydrogen bonds (so for example 2,6-diaminopurine instead of adenine).

The final issue is explained by Orgel [45]: The existing and proposed autocatalytic metabolic cycles for autothrophy can only work if every single step has only very few irreversible side reactions talking material out of the cycle. This finally requires a high specificity of the mineral surface catalysts, which is nearly impossible to expect.

No, I did not want to make ad hoc assumptions.

To avoid a chaotic discussion I have split my thoughts into two discussions topics (both in this forum):

 

1)

http://www.scienceforums.net/topic/71735-early-life-life-could-only-originate-early-or-not-at-all/

 

2)

this topic

 

This topic here is very speculative.

The topic 1 is more serious (and is my main topic). There I claim that life could only emerge early or not at all. Please have a look at it. You can start discussion there.

 

Here I wanted to discuss the consequences:

 

Is extraterrestrial life still probable, even if we assume that early emergence of life does not indicate anything?

(because life could only originate under the conditions of early earth.)

 

looking forward to your comments

Jens

Agreed.

Phylogeny of paralogs makes sense. But you should be very careful with the perceived order of the branching points.

 

Yes, beeing orthologous is a fundamental assumption. But people tend to forget this in practice.

Here it is an example where it is claimed that the phosphoseryl pathway is a a feature left from LUCA, even though looking into the real biological situation, there are really all the pieces of the puzzle available (at least from my point of view you could hardly ask for more evidence) to indicate that it is a late optimization.

 

Maybe I am simplifying too much but this is what I want to say with regards of method:

• If there is an old relationship (e.g. older than the 800 million years) to investigate, you cannot deduct anything out of non-functional conserved regions because they are randomized.
• If you include paralogs, the outcome will always be that splitting was before LUCA (even though that is actually not the case). At least the tree will always be biased in a way that it predicts splitting earlier than it actually was.
• Even for orthologous genes there is a risk of this issue, because functionality is not only the main catalytic functionality but also the additional regulatory functionality, which is often much less understood. This means that two proteins which are orthologous from the main functionality are actually like paralogs for some regulative functionality (different regulation in other species, binding to different other proteins or RNAs, ...)

I am saying life as such is rare.

 

(because the early origin was the only possibility: see topic http://www.scienceforums.net/topic/71735-early-life-life-could-only-originate-early-or-not-at-all/ )

 

I do not think that complex life is rare (once there is life at all).

 

However, as mentioned above: This is really very speculative .

It does not seem to obvious to many:

At least scientists can publish such (to my understanding -- misinterpreting) results in PNAS:

Reference [9]: O’Donoghue P, Sethi A, Woese CR, Luthey-Schulten ZA (2005) The evolutionary history of Cys-tRNA^Cys formation. Proc Natl Acad Sci U S A 102: 19003-19008. doi:10.1073/pnas.0509617102

 

I agree to you that there seem to be a consensus that phylogenetic trees of whole species (and not of individual proteins or rRNAs which this is about) do not show the same pattern and there is in some cases really uncerntainty.

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This is a much more speculative side topic to the main topic “Early Life! -- Life could only originate early or not at all.”

If you question the thesis of the main topic, read the details and post a comment in the main topic – not here.

This topic is a discussion under the assumption that the thesis in the main topic is right:

• Life could only originate early during meteorite bombardment (and not later).
• Life originated on Earth and not from another planet.

This means we cannot deduct from early emergence of life that origin of life is a likely event.

 

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Full text with all the references and details

 

Abstract

The thesis presented in ‘Early Life’ implies that life could only emerge during the meteorite bombardment and not after it ended. Typically it is assumed that life emerges on all Earth-like planets. However, the only reason for this assumption is that life emerged so early on Earth. This is taken as prove that life emerges everywhere, if the environment is suitable. If we now have to assume that life could only emerge very early on Earth and not later, this means, we cannot deduct from early emergence of life that origin of life is a likely event. In contrast the more you investigate the details of the biochemistry of metabolism, replication, transcription and translation, the more you see stunning complexity, which cannot be reduced in a simple way. Even the most primitive looking life forms are not primitive at all. With the current knowledge, we have to assume that the emergence of life is an incredibly unlikely event.

 

Life is Rare

The usual argumentation – especially in astronomy – for how likely you can find life outside Earth goes as follows:

 

Contra existence of extraterrestrial life:

A) If life has originated on every suitable planet in our galaxy, there should be some planets which have evolved intelligent life for example 100 million years before humans and should have colonized the galaxy already. So we either should already have had contact or we should not exist at all. This argument has been disputed: The evolution of complex higher life forms is unlikely and that is the reason why we do not have seen any other intelligent life elsewhere. The evolution of complex multicellular life forms requires a constant temperature range over some hundreds of millions years, which is more difficult to obtain than one might think. Indeed it looks that not only the exact distance to the sun but also a stabilizing big moon and a protecting big planet like Jupiter and roughly the right amount of mass-extinction events are needed. However, you can also argue that emergence of complex animal-like higher life forms is no issue at all since this event mainly depends on oxygen level which was reached only about 1000 million years ago. In addition the authors of Rare Earth are likely to underestimate the power of life in assuming that roughly 45°C is the upper limit for complex life. The upper limit can easily be 60°C (or more) and the only reason for not having complex life on Earth in this temperature range is that the habitats with this temperature are rather small (center of hot springs) or dry. There are for example multicellular fungi which can live in human-made piles of organic matter up to 60°C, which show that Eukarya can actually survive such temperatures. This makes it likely that given the proper large and humid environment also more complex life forms could survive temperatures much higher than 45 °C.

 

B) Even though the current knowledge in science of the biochemistry of life is already very detailed it looks actually nearly impossible that a self-replicating system can appear spontaneously (see chapter Details V below). The statement of Francis Crick ‘At present, the gap from the primal „soup“ to the first RNA system capable of natural selection looks forbiddingly wide’ is still very true!

 

Pro existence extraterrestrial life:

C) Life originated very early on Earth, this means origin of life is simple and will happen under every suitable environment.

 

In this article I try to show that emergence of life could only happen early or not at all. This in turn means that there is no prove at all that emergence of life is something that happens easily and this means also that argument C is not valid.

 

In contrast we have to take the biochemical evidence for argument B (see page 2 chapter ‘Details V: Why is the Emergence of Life an Unlikely Event’) into account, even if the result is not what we might wish. Therefore I think that:

• It is likely that Earth is the only planet with life in our galaxy.
• There will be no life found, neither on Jupiter’s moon Europa (which probably has a layer of liquid water underneath ice) nor on Mars
• We will not find extraterrestrial planets with a spectrum indicating high oxygen (O₂) concentration in the atmosphere (which in turn indicates existence of life).
• We will not be able to re-produce the origin of life in vitro

We should consider seriously that we are alone and that Earth is the only planet where we can live (without waiting some ten thousand to million years of terra-forming of another planet with liquid water). Life is a very unique thing. We simply do not realize this, since we are so used to it.

Of course those statements cannot be proven yet and cannot be deducted without doubt based on current data. However, even under scientists it has become so common to state that there must be life on every suitable planet, that I feel a strong statement against this is necessary to keep the focus on the currently known facts. We should do so even if we (including myself) might which it were different.

Since it is quite possible that in our galaxy life is unique on Earth we should consider investing more in protecting this heritage by any means (protecting habitats, seed banks, genetic libraries, and taxonomy research projects of higher organisms and especially in microbiology).

This is an attempt to jointly (in this forum) sketch a most likely scenario for origin of life

 

 

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Let’s jointly sketch a most likely scenario for the origin of life. Since the origin of life is a historic event, the target is not to prove anything but to achieve plausibility.

I am looking forward to your comments / critics / opinions

 

How to structure the discussion:

• I have sketched a most likely scenario for the origin of life from my point of view as a starting point for the discussion.
• Read the abstract provided below (in this first post)
• Before you make a comment to a specific topic read the corresponding chapter (follow the links to the pdf document). It is only 2 pages per chapter.
• Any critics, better ideas, supporting ideas are very welcome. I am very well willing to change my point of view.
• In case the discussion is constructive, I will summarize and update the document by mentioning your user names as source of the corresponding change (of course only, if you agree)

Please do not:

• Post any comments on how probable or improbable extraterrestrial life is -> use the speculative topic “Lonely Life? – Is Earth the only planet with life in our galaxy?” instead (it is in the same forum).
• Claim that nothing can be proven, or nothing is known, or everything is pure speculation. (means you have not even read the 3rd sentence of this topic )
• Post critics without reading the detailed chapters. (I have no problems with critics, but if my only answer is either to include the complete detailed chapter in every answer, or answering that you should read it, the whole topic becomes unreadable for all the others.)

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I try to show that life already evolved during the time of disastrous meteorite impacts which nearly sterilized the whole Earth by boiling and evaporating most of the liquid water. This is in contrast to the usual unquestioned assumption that early life evolved after the meteorite bombardment of early Earth calmed down and stable oceans were present.

The proposed scenario of origin of life

The proposed scenario of origin of life comprises the following steps:

1. Early Start. Evolution of life did not start started after the meteorite bombardment of early Earth calmed done and stable oceans were present. In contrast it started right with the first presence of liquid water. The typically called hostile environment of early Earth indeed was not preventing the evolution of life but in contrast was absolutely necessary for evolution of life.
2. Concentration. Heavy meteorite impact events literally boiled some of the oceans (on global scale) or water reservoirs (on regional or local scale). Additionally strong volcanic activities had the same effect on regional and local scale. Thereby all the organic precursor molecules present where concentrated and condensed to energy rich bigger molecules. Only very few life forms survived.
3. Dilution. After the impact event the surface of the Earth cooled down again and liquid water again was present in big amounts. The remaining life forms benefit from an enormous amount of high energy condensed molecules. So after each event an extremely energy rich primal soup was available to the survivors.
4. Evolution. Those few survivors had nearly no competition and therefore could undergo rapid evolution until the next event happens.

 

 

Steps 2 to 4 were repeated multiple times on local, regional and global scale. The following evolutional phases were made across multiple of those cycles above as shown in the Figure: a) RNA-based life forms (bound on rocks). b) The translation was invented initially with a very small set of amino acids. c) More and more amino acids were introduced in translation. There were multiple life forms present at the same time with different numbers of amino acids actually used. d) In a catastrophic global event only very few (preferentially thermophilic) life forms survived which had the genetic code as known today. Other life forms with less amino acids (or even more) or a different encoding did not survive. e) The few survivors with the homogeneous genetic code evolved further. The first living cells emerged only after this catastrophic global event by developing cell membrane biosynthesis as two independent ‘inventions’ for Bacteria and Archaea. {see page 1 in “Early Life”}

 

The main reasons for this thesis are:

• The unexpected uniformity of the genetic code, which indicates either a near extinction event or extra-terrestrial origin of life or massive horizontal gene transfer.
  {see page 3 chapter “Details I: the unexpected uniformity of the genetic code”} The chapter Details I also contains a reasoning why horizontal gene transfer is less plausible as source for the uniformity of the genetic code.
• The two fundamentally different forms of cell membranes, which indicate that life started on Earth and not on another planet.
  {see page 5 chapter “Details II: The two fundamentally different forms of cell membranes”}
• The much bigger evolution speed needed to explain all the fundamental "inventions" which lead to the first living cells. Evolution always made great steps in short time when there was a large environment open to conquer without competition by other life forms already present. The temporary and nearly Earth-wide repetitive absence of competition (caused by the bombardment) is the most perfect environment you can think of to make giant steps in evolution.
  {see page 8 chapter “Details III: Evolution Speed”}
• Local heat-caused concentration produces both polymers and high energy molecules to sustain primitive life forms with all kinds of building blocks after dilution.
  {see page 10 chapter “Details IV: The need for high energy molecules to start life”} The chapter Details IV also contains a reasoning why autotrophic origin of life as an autocatalytic chemical cycle is less plausible.

The phosphoseryl-tRNA pathway of Cys synthesis is a late energy optimization of the methanogens and not a feature of LUCA or

-- How Paralogs Bias Phylogenetic Trees --

 

Full text (7 pages) with all the references and details

 

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During my text research on origin of life, I often found people claiming that phylogenetic trees prove early origin of some features. In many cases this looked very strange to me. Here I have a case in which – at least from my point of view – evidence is clearly against the interpretation of the phylogenetic tree. Please read through the text provided as link to a pdf document and comment, if you see errors in my argumentation or additional info for this hypothesis.

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In this document it is shown that the phosphoseryl-tRNA pathway of cysteine synthesis is clearly a late energy optimization of the methanogens and not a feature of the last universal common ancestor (LUCA) as currently claimed. Chapter VI contains an (hopefully) easy to read explanation (without mathematics) how paralogs bias phylogenetic trees (and systematically lead to these wrong claims, which have not been questioned so far). I hope the biologist community will take this into account more often in future and that a more critical approach to "sure" mathematical results (based on false unmentioned assumptions) becomes more common (see ‘Amino Acid Usage Cannot Prove Hyperthermophile Origin’ in ‘Early Life’ for another case).

 

Pyrrolysine

[5,6] In contrast to selenocysteine pyrrolysine (Pyl) is found primarily in some methanogenic Archaea and only in very few anaerobic Bacteria. There is a claim [7] that pyrrolysine is very ancient and before LUCA, based on a calculated phylogenetic tree (based on high-quality sequence alignment obtained through 3D-stuctures). But the biological data indicates that it is a late change of the genetic code which happened in a branch of Archaea and then was horizontally transferred to the few Bacteria living in same habitats for the following reasons:

• In those methanogenic Archaea the stop codon UAG has been reassigned to code for Pyl, in contrast to the bacterium Desulfitobacterium hafniense in which UAG still has the meaning of a stop codon in most proteins [8]. This is the exact behavior to be expected in case of a late horizontal gene transfer to a predecessor of Desulfitobacterium hafniense and not in the case of inheritance.
• ‘The high conservation of the Pyl gene cluster and the small number of organisms that utilize Pyl suggest its relatively recent origin’ as stated by [8].

 

Phospho-Seryl-tRNA Pathway of Cys Synthesis

There is an analogous claim by O’Donoghue [9] that the charging of tRNACys via O-phospho-seryl-tRNACys (Sep-tRNACys) has been evolved before LUCA. Instead it looks much more that the Sep-tRNACys pathway has evolved together with the first methanogens (and not before LUCA) for the following reasons:

• The genes of this pathway occur only in a very restraint group of methanogenic Archaea and not widespread in Archaea, Bacteria and Eucarya. The close evolutional relationship between the methanogenic genes and the Sep-tRNACys pathway was already remarked by O’Donoghue [9] himself.
• This pathway saves 2 ATP compared to the O-acetyl-serine pathway and at least 4 ATP compared to the cystathionine pathway (see Figure 4 and legend). So it is not a relic of an old, sub-optimal way to charge tRNAs but rather an energetic optimization introduced at time of the first methanogenic Archaea.
• The price for this energy savings is that there are thermodynamic issues with the Sep-tRNACys pathway as soon as the H₂S concentration is too low, because in all the other pathways the reaction step incorporating H₂S is based on an acetyl ester, which is more energy rich than a phospho-ester. This means the Sep-tRNACys pathway is only suited for environments with high sulfide concentrations. Methanogenic Archaea are actually living in such environments and the only non-methanogenic archaeon (Archaeoglobus fulgidus) with the Sep-tRNACys pathway is actually a sulfide producer (and still has most of the methanogenic genes).
• This is perfectly in line with the fact that the O-acetyl-serine pathway has proven to be inhibited by H₂S [10] in the archaeon Methanosarcina thermophila, a fact was surprising [10] and could not be explained so far. This means the O-acetyl-serine pathway is regulated down under conditions in which the energetically more favorable Sep-tRNACys pathway can work efficiently. This also explains why it makes perfect sense at least for some methanogens to keep both pathways.
• Even though a difference of 2 ATP is huge (the whole methanogenesis of is just 1 ATP better than acetogenesis), you might argue it is not much, since cysteine synthesis is not part of primary energy metabolism. However, there is recent evidence that the methanogenic Archaea using this new pathway have twice as much need for Cys as usual organisms [11], pointing out the importance of sulfur metabolism for methanogens.

Conclusion

How can it be, that in both cases (Pyrrolysine and the Sep-tRNACys pathway) only the phylo-genetic tree predictions do not fit into the picture? This is – I think -- because all phylogenetic tree prediction methods are systematically biased to predict all splitting of paralogs before LUCA, even and especially if there is no phylogenetic information left any more (see page 3 chapter Details VI).

 

(for explanation follow the link to the Details VI chapter.)

 

I assume it is too late now for your homework.

But for the other readers, here is what I see out of your spectrum:

• The huge peak of H₂O between 4 and 5 ppm is completly missing -> This means your spectrum has been taken in D₂O instead of H₂O (and multiple cycles of lyophilisation to completly exchange any H by D). Deuterium shows no signals. --> Since D2O quickly exchanges with any NH groups, you have no signals for NH groups under such conditions either. --> "amides (backbone HN)" and "sidechain HN" of your legend are not visible. --> This means all signals in that area are coming from aromatic sidechains (or some stronger than usual shifted H_alpha.)
• The spectrum shows a lot of broad peaks and at ppm values far from standard values --> This means the protein is well folded and not denatured.
• The peaks at 0 ppm and below are all coming from aliphatic H atoms that are directly near an aromatic ring in the 3D folding of the protein. The sharp thin single peaks are from methyl groups. The broader peaks from CH₂ groups (which rotate less quickly).
• At many ppm values (especially between 0.7 and 4.7 ppm) signals from different H atoms overlap. Structural relationships therefore cannot be deducted out of this spectrum.
• Aliphatic side chains H atoms show the highest peaks because there are more of them than of the aromatic H atoms and the H_alpha.
• Sharpest and therefore highest individual signals are typically coming from the methyl groups in Met, since they rotate freely as all other methyl groups and show no splitting because of neighboring covalent H-atoms (since the next atom is an S-atom with no H-atoms bound to it). However, individual signals in that area are not necessarily resolved in this spectrum.

That a gay male has a more feminine, feminized, or female-altered brain than a straight male should not be assumed. There is very little evidence of that, and most of it barely reasonable much less rigorous.

 

O.k. I am really no expert on this topic and have not read enough scientific literature about it.

My argumentation was just founded on my personal contacts to gay men and what I have read in some books written by gay men about gay men. --> leading to my personal opinion that at least the majority of gay men are not just exactly like heterosexual men with the only difference that they are attracted by men instead of women. The difference really seems to be more than that. However, assuming out of this a "female" brain in a male body is probably too simplistic.

You are welcome.

 

If you are really interested, you should of course also read about the "mainstream" opinion of abiogenesis:

So I recommend to read some of the articles of RNA worlds.

 

There is also an "outsider" (Wächtershäuser) who is trying to provide real details about why life is inevitable (from his point of view):

Life in a Ligand sphere. and Life as we don't know it.

 

 

I am currently very busy. But before the end of the year I will post my complete thoughts about abiogenesis in this forum.

@lowten:

I agree to all your points.

 

...besides that I think the EU is still making progress (even though very slowly).

 

Especially the Bologna Process to set up a framework which makes it easier for students to switch universities in Europe is a good thing. (Even though there are of course still a lot of universities, which try to do their best to make it impossible for students to go somewhere else after the bachelor.)

Small correction of my thoughts to scetch one a bit more likely scenario (for most of the cases of gay men):

 

- There might be a regulation system changing the "female brain" (seem to be the default) to a "male brain". This is probably done very early (before or after birth) and can only happen in a certain point of time (after that the "male brain" genes cannot be activated any more).

- "female brain" also means beeing attracted by men and "male brain" means beeing attracted by women (hard coded -- no choice).

- This probably involves multiple loci on the DNA, since long RNAs (not visible as genes) and proteins probably are involved (like e.g. for X chromosome inactivation). This makes it more difficult to trace genetically.

- There are variants of those loci (RNA and protein) which together mean that the switch to "male brain" does not work in 100% of the cases but more or less randomly take place or not (in the critical time frame).

- The relative frequence of those variants might actually be a result of evolution (equilibrium between disadvantage of having no children and advantage of group selection -- see my post Nov 4th). With this regards it is no "error" but a feature.

 

This scenario explains:

- its heritable but only with 50% in homozygotic twins

- the heritage pattern is complex and no obvious "gay gene" can be found.

- most homosexual men say that they have always been like this -- clearly before puberty -- and never made a choice.

- Of course a "female brain" in a male body with male hormon levels is something different than a "female brain" in a body with femal hormone levels, but most gay men also have other behaviour which differs them from heterosexual men -- not only by beeing attracted by the same sex. So it is not the imprinting process alone (if there is really any).

- the high percentage of estimated homosexuality.

 

Of course there are probably many other scenarios which can also explain the facts. (I have not studied the literature about it. I just combine what was written here before)

 

...and if a long RNA is part of it, they are not detectable as genes and easily to be overseen as supposed "junk DNA"...

 

 

At Jens

 

You give me right that I Have a DNA error?

 

 

The data mentioned in this thread (~50% gay within monzygotic twins) looks like my assumption B (see my post from Nov 4th) might actually be close to reality.

However, I do not claim to really have an overview on the available data in this field.

So yes, I think, you might have a DNA "error".

(if you really insist in calling it "error". But see also what I have written, why it also seems to be something useful, since 4% is definitely too high.)

generic info (to be applied to your case, to be combined with your chemical know-how):

 

- all H atoms are visible (also those in H₂O). Deuterium does not give any signals.

- broader peaks indicate that the H atom(s) move less than narrow peaks

- multiple H atoms at the exactly same shift value (ppm) sum up to big peaks

- the shift values of the H atoms can deviate from standard values depending on their environment in space. In practise especially neighboring aromatic rings are the source of strong changes of the shift values. The strongest shift changes are produced by Tryptophane (Trp, W).

- the 3 H atoms in methyl groups always produce only one peak, since they rotate too quick (even in the center of proteins) so that all of them always "see" the same neighborhood.

 

There is a small story to tell on your spectrum, but you have to find out (or at least make the first steps).

 

hope this helps more.

 

...I will not tell more until you make a proposal....

(On a one-dimensional NMR spectrum of a complete protein you cannot really see much, because it is completly overcrowded.)

 

To discuss it you should proceed as follows:

• Search for the standard shift values of the amino acid side chains (you should have this in your books or received as input, or use google scholar)
• What you actually see is quite different in some cases. Think about it and make some proposals here. Once you have done this, I will point you to more answers. (Since for good reasons I am not allowed to do your homework in this thread

The parameters to consider are everything you can see in this spectrum:

- ppm value of the peak (mainly)

- heigth of the peak

- width of the peak

- potential artifacts (H2O)

 

What does the spectrum tell you about the protein?

Under which conditions it has been recorderd? (what do you expect to see under this conditions?)

How would the spectrum look like, if the protein had been denatured?

Your test does not reflect the situation in cities. The gasoline is burned. Not much is evaporating unburned.

 

However, if you still want to do it like this:

Make sure that really no gasoline is accidentially going as liquid into the soil of the plants as otherwise the effect you want to measure is actually caused by killing roots with liqid gasoline and not by the gases. If your plants are dieing to quickly just use a bowl with much smaller surface (assuming that you aquarium is not completly closed on top).

Higher temperature will simply lead to more gases evaporating....

No conspiracy needed.

 

Agreed.

 

To avoid getting paranoid, it helps to apply the following sentence in many matters of life:

 

"Never attribute to evil what you can attribute to incompetency."

 

So if in recent German school books about the topic "Great Depression 1929" the stock exchange speculation bubble is not even mentioned as cause, you could assume a conspiration of the world wide banking system that still wants to continue with their speculations world wide and try to influence the authors of school books. However, applying the rule above it is much more likely that the author of the schoolbook was simply very theoretic and far from real life.

 

And with regards to university level text books:

While manipulation of school books (e.g. by religous fundamentalists) is at least a potential danger, nobody will invest the work to manipulate university level books (less people, and more difficult to manipulate).

The reality is much more that the highly skilled authors invest a lot of their time, energy and love to the topic to write them, without getting much back (especially not with regards of money).

The reference for Carls Woese theory of the reasons for a unique genetic code is here:

Collective evolution and the genetic code

(Thanks to Carl Woese publishing in PNAS everybody can read publicly funded research results without paying 30$ for every article )

My personal abstract on this (but if you are really interested, read it, because I am not convinced):

 

It is impossible that the genetic code (i.e. the translation of base sequences into amino acid sequence) started with the same precision as it has today. Neither the early form of ribosomes nor the early form of aminoacyl transferases could have the perfection they have today. (aminoacyl transferases are typically double enzymes with a charging and a proofreading catalysis function, to reduce errors to a minimum. So current aminoacyl transferases make less errors than even theoretically possible with one active catalytic center). So there must be some evolution towards a more precise translation. Assuming that horizontal gene transfer played an important role in early evolution, this means that a collective evolution should point into one unique genetic code, even if started from multiple slightly different but unprecise genetic codes. The biggest gene pool gets more and more innovations than the smaller gene pools using a really incompatible genetic code. This is why only one genetic code will survive. Once the organisms have reached a certain level of complexity (the "Darwinian Threshold" introduced by Woese) it was not advantagous to participate in this massive horizontal gene transfer, because all the genes have reached a high level of perfect interaction. This is the point the vertical descendance started and the 3 domains "Bacteria", "Archaea", "Eucarya" branched out of this pool.

 

Note: In case you do not know: Carl Woese is the one who found out that Archaea are something completly else than Bacteria:

Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya

 

To get a complete picture you should also read:

Horizontal gene transfer: A critical view

 

My personal opionion is much more on the side of the last article. However, make up your mind yourself.