Paradigm shifts in the world of biology- evolution of proteins

At the moment the race is on to prove that the biochemical compounds got kick-started, not by earthly processes, but by organic molecules arriving on comets. I must admit I have my doubts as to the relative impact of cometary compounds compared to the contribution of Earth’s geological processes creating a complex mix of chemicals ready to create the “primordial soup” for life.  Of course biological structures are chemically based, and comply with both the laws of physics and chemistry (and maths) so far as one is aware anyhow (they seem to be able to slow down entropy).

The planet was synthesized as the solar system formed about 4.5 Ga, creating toxic conditions that prevented life from arising for another billion years or so, such as high levels of methane in the atmosphere.  There are Bacteria and other forms of life, including multicellular life, which form another Kingdom containing plants, animals and fungi, in which hominids are found. However, there is another Kingdom, that of the unicellular organisms Archaea which are ubiquitous on the planet. These and some forms of Bacteria do not photosynthesise, but utilise chemicals, and some of these are called chemotrophs whilst some are called Methanogens, because they utillise chemical substances to produce methane.

A lot of these are found in extreme environments, especially Archaea which tend to like toxic conditions. These types of Bacteria and Archaea are the ones that probably were the earliest ones when Earth was toxic. When comets were bringing in toxic organic molecules like formaldehyde. But after Earth stabilised as a whole rock, which was a good billion years earlier than when the first fossil unicellular organisms are found. So it took a billion years for the processes to occur that resulted in life, and one must ask what may be involved.  That life was therefore not the cyanobacteria, the unicellular organisms which by developing photosynthesis oxygenated the planet, making it possible for many lifeforms to develop by using the nascent oxygen of the atmosphere. Flamingos turn pink due to eating such “algae”- an erroneous term that should never be used in the context of cyanobacteria. Cyanobacteria which photosynthesized arose yet another billion years after the original unicellular organisms, c. 2.4 Ga.

There is a difference between methanogens which produce methane and other chemotrophs and the type of protocells which must have developed on the early Earth. It is clear the latter must have found a way to utilise the toxic compounds available. Thus I think that if people are looking for methanogens such as on Mars where the production of methane was sought as evidence of life, they may have it the wrong way around. What is needed is an organism that can somehow utilise toxic conditions and/or a toxic atmosphere, not ones that can produce it! Such organisms that may have existed for the first billion years of toxic Earth, surviving and feeding off what was available! Which wasn’t oxygen, since it took a further billion years after life evolved, for unicellular bacteria to figure out how to split the water molecule, and for them to learn to use the carbon dioxide in the atmosphere in photosynthesis.

Therefore one is looking at another kind of unicellular organism to start the Life show off.  The organism I suggest may have been anaerobic methanotrophs as there was no oxygen but a lot of methane in the early toxic Earth.  Wikipedia describes these on the page “Methanotroph” (https://en.wikipedia.org/wiki/Methanotroph), including references.  Excerpts have been repeated here for explanatory purposes, with some modification for further explanation:

(from Wikipedia): Methanotrophs oxidize methane by first initiating reduction of an oxygen atom to H2O2 and transformation of methane to CH3OH using methane monooxygenases (MMOs, enzymes) . Differences in the method of formaldehyde fixation and membrane structure divide the methanotrophs into several groups. Methane-oxidizing bacteria have been separated into four subgroups: two methane-assimilating bacteria (MAB) groups, the methanotrophs, and two autotrophic ammonia-oxidizing bacteria (AAOB). Investigations in marine environments revealed that methane can be oxidized anaerobically (Anaerobic Oxidation of Methane or AOM) by a consortia of methane-oxidizing Archaea and sulfate-reducing Bacteria. The exact mechanism of methane oxidation under anaerobic conditions is still a topic of debate but the most widely accepted theory is that the Archaea use the reversed methanogenesis pathway to produce carbon dioxide and another, unknown substance. Ettwig et al. found a bacterium oxidizes methane anaerobically without a partner, probably by utilizing the oxygen produced internally from the dismutation of nitric oxide into nitrogen and oxygen gas.
Wikipedia further describes this process in its page “Anaerobic oxidation of methane” (https://en.wikipedia.org/wiki/Anaerobic_oxidation_of_methane), excerpts from which are similarly provided:
(from Wikipedia): AOM occurs in anoxic marine and freshwater sediments. During AOM methane is oxidized with different terminal electron acceptors such as sulfate, nitrate, nitrite and metals. ANME stands for “anaerobic methanotroph”. Recently, ANME-2d is shown to be responsible for nitrate-driven AOM without a partner organism via reverse methanogenesis with nitrate as the terminal electron acceptor, using genes for nitrate reduction that have been laterally transferred from a bacterial donor. In 2010, omics analysis showed that nitrite reduction can be coupled to methane oxidation by a single Bacterial species, NC10, without the need for an Archaeal partner.

Recent research has just changed the ball-game for how life developed on Earth.  Forsythe et al. (described in Science Daily as  “Finding the origins of life in a drying puddle http://www.sciencedaily.com/releases/2015/07/150720094522.htm  July 20, 2015; link to 2015 paper below) produced polypeptides in wetting and drying conditions, with the likelihood being that proteins evolved on terrestrial Earth and not in the oceans as previously envisaged.  This confirmed to me the importance of the role evaporation in life’s evolution.

Although it is very interesting that a puddle containing the necessary ingredients may have been available for evaporative and hydrating processes to work on, creating polypeptides and later complex proteins in terrestrial zones, that does not per se mean that life itself i.e. the initial protocell, arose terrestrially.  Life may still have arisen in the oceans, but this would necessitate the “puddles” being nearby to an ocean, so that coastal inundation could have swept the new proteins into the ocean.  There they then would have to have replicated to become abundant enough to reach locations where life formed, e.g. deepsea vents, indicating that RNA may have preceded life. If however the process of polypeptide formation leading to proteins led to life on land, then RNA may have arisen at an early stage after it did so.

These timelines, processes and organisms have implications for how these processes may occur on other planets.  It is interesting to speculate that on other planets somewhere in the Universe, the conditions (gases etc.) may not be entirely chemically produced. They could, from our knowledge of life on Earth, involve the production of oxygen for an advanced evolutionary atmosphere, and the production of carbon dioxide from methane for an earlier, toxic one.  All that is needed for the production of proteins is apparently a puddle undergoing drying and wetting.   But I am a skeptic unfortunately about the prospects of there being life on any other planet!

All this leads me to speculate as to what happened next.  I mean in the puddle.  Previously I had thought that a membrane may have begun, which was the precursor to the cell wall, by a water or water-metallic membrane forming between two rocks, eventually closing around like a bubble.  This could have occurred at the vents for example.  However if proteins evolved in puddles, whether on the coast or inland, the next step for complex proteins might have been protective mechanisms.  From drying out that is, or from inundation for that matter.  To avoid evaporative damage or solar UV damage, proteins may have evolved protective structures.  These may initially have been in the form of simple lipid structures, and lipids are hydrophobic so keep water out, but may also prevent leachiing of water and nutrients.  So if the team of researchers can form proteins in the puddle it might be interesting to see what happens if they add a few lipids to the mix.

Either way it seems to me that coastal environments are favored, particularly those in which metallic elements are readily available, such as the volcanic salt lakes of eastern Africa.  If one follows up the anaerobic methanotroph theory, elements were definitely needed for bacteria, and may have been for some protein development earlier.  For example see the excellent review by Hanson and Hanson in the references below for the importance of copper to methanotrophs.  Previously I thought that such evaporative lakes may have been the site of eukaryote (multicellular) evolution, however it now appears that marine conditions may not necessarily have been involved for evolution of prokaryotes before them.

However fossil evidence of early bacteria indicate that the marine environment is indeed likely to have been the site for evolution of life and its radiation.  This presents a conundrum as newly evolved proteins in puddles must get from land to sea, inferring coastal inundation processes.  And they must be capable of replication, inferring the evolution of RNA replicative processes prior to the evolution of life.

REFERENCES

Forsythe, Jay G. et al. (2015): “Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth”; Angewandte Chemie International Edition (early version online: http://onlinelibrary.wiley.com/doi/10.1002/anie.201503792/abstract).

References given by Wikipedia worth following up:
Ettwig, K. F.; Butler, M. K.; Le Paslier, D.; Pelletier, E.; Mangenot, S.; Kuypers, M. M. M.; Schreiber, F.; Dutilh, B. E.; Zedelius, J.; De Beer, D.; Gloerich, J.; Wessels, H. J. C. T.; Van Alen, T.; Luesken, F.; Wu, M. L.; Van De Pas-Schoonen, K. T.; Op Den Camp, H. J. M.; Janssen-Megens, E. M.; Francoijs, K. J.; Stunnenberg, H.; Weissenbach, J.; Jetten, M. S. M.; Strous, M. (2010). “Nitrite-driven anaerobic methane oxidation by oxygenic bacteria”. Nature 464 (7288): 543–548. doi:10.1038/nature08883.
Hanson, R. S. and Hanson, T. E. (1996). “Methanotrophic bacteria”. Microbiological reviews 60 (2): 439–471.

Haroon, M.F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P., et al. (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500: 567–570.

Reimann, Joachim; Jetten, Mike S.M.; Keltjens, Jan T. (2015). “Chapter 7, Section 4 Enzymes in Nitrite-driven Methane Oxidation”. In Peter M.H. Kroneck and Martha E. Sosa Torres. Sustaining Life on Planet Earth: Metalloenzymes Mastering Dioxygen and Other Chewy Gases. Metal Ions in Life Sciences 15. Springer. pp. 281–302. doi:10.1007/978-3-319-12415-5_7

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Entropy in biological systems

   This post is based on ideas I had in relationship to a (very sophisticated) website discussion on the views of England (and associated discussion through posts) of entropy and biological systems which you will find at http://www.simonsfoundation.org/quanta/20140122-a-new-physics-theory-of-life/#comment-159978

    The original state was a physical state and not a biological one until life prevailed and as such must obey all known physics rules. However the possibility exists that early organisms may have initially overcome some of the constraints of the physical universe, or at least to minimise them. This is where the concepts of England and others regarding entropy must be invoked, if not later to describe ecological systems. 
   I have been greatly perturbed by the constant use of “equilibrium” forest ecosystems etc. and it is very difficult going from the molecular, to the macro level of organisation of microbial communities or forests, but at the micro level effectively if something is at equilibrium it is dead. Kauffman described the possibility that dynamical non-equilibrium systems could be stable, which seems to me a better description for forests and other ecosystems i.e. at the macro level. Whatever consensus is eventually reached the molecular to the ecosystem level should be consistent in the final thesis. Except that we all know that Einstein/gravity and the quantum world aren’t that consistent! So do we have to await the outcome of those investigations before we assign Boltzmann to the wider world of soil bacterial communities? It seems to me that until physics resolves that dilemma it will be quite plausible to differentiate macro and micro systems, especially in the biological world which attempts to control the physical (albeit with various success levels). 
    The new theories of life based on entropy could be maligned, but then that is what was done to the chemical theory of life 50 years ago. There are coupled chemical and physical conditions which occurred when life first arose as mentioned. But life is another system which often overcomes or utilizes or improves physicochemical conditions for its own purposes. Of course it must ultimately be accountable to physics processes such as entropy and this may indeed be a driving factor in the organisation of some or most ecosystems and communities, but perhaps not in ways proposed by England and others. 
   There is still the problem of the original sentient organism though. Much investigation has been done on chemical factors involved such as the ATP system and H systems, and also on heavy metals, so that early organisms could have arisen primarily in response to chemical factors. The fundamental nutrient requirements of nascent life really needs to be clarified before we can make any estimates regarding chemical equations etc., and thus energy and entropy. The truth is we don’t really know the chemical equations, although there is acknowledgement that RNA was involved early on. Personally I think the entropy outcomes of the ADP/ATP system which is shared by all lifeforms is important.
  When life began I don’t think one could call the first precursor of the protocell an “ecosystem”, so we are definitely not dealing with the macro level there, but probably with the micro level and the equilibrium Boltzmann equations.  My view is that the early cell progenitor probably arose as a chemical system under a membrane between rock surfaces, which became coordinated to the point where it behaved as one entity and thereafter formed a more permanent membrane.  This precursor to the proto-cell must not have been singular, so that a number of such chemical “bubbles” existed.  They began to “trade” scarce nutrients with each other, although which ones were scarce is not clear, perhaps you do have a nascent ecosystem, involving entropy at the macro level.
  One thing I noted I think from  Lehninger’s biochemistry books was in regard to the excess of energy that plants have to deal with. Additionally the entire mitochondrial ATP energy system of animals is also set up to deal with exactly what the article described, dissipating energy, but not in the sense proposed. The problem is too much energy. Plants cannot deal with the amount energy provided daily, and animal mitochondria cannot either.  Both deal with this via stepped processes involving many chemical equations.  But are these two major biology energy production systems ultimately driven to produce net entropy?
   After the nascent filmy bubble of chemicals coalesced and later formed a protocell complete with RNA, they were no longer ever again purely physical. There is something of a split in science where entire systems are studied by either physical scientists or biologists noticeably in carbon chemistry where some see the problem as a purely physical/chemical study, whilst others are only interested in microbial or plant production systems. Any theory that proposes to describe life cannot be a purely physical theory as lifeforms are sentient.
    Even the most primitive bacteria has sophisticated responses, and one of these is to move away from the pipette- to survive. It is as though life is a response system to the physical environment.  Thus theories of life may incorporate mathematics and physics, including concepts such as entropy, but if the life system is a response system, it may have qualities that are unique also, and these must be incorporated into descriptions of the system e.g. sentience.  It is also dangerous to degrade the biosphere, because the physical system will then have more influence than the life system on the planet again i.e. in two interacting systems one may be more dominant. Only by maintaining biosphere resilience can we avoid the worst physicochemical excesses, and even then not always, such as in the case of earthquakes etc. so that it is clear that in spite of the life system’s best efforts, the physical system retains its dominance, at least to some extent.  This begs the question to what extent is the life system and the physical system one as in the case of Gaia, or to what extent are they two interacting systems.
   This is a question that should be answered by a similar body to international synchotrons e.g. an international Biotron. Surely the systems involved on the very planet we live on are essential for us to understand, and only then can we really understand how land-ocean-atmosphere interactions behave in the sense of climate change etc. My view is that James Lovelock was on the right track with “Gaia” but went a bit too far, and the systems are still separate but very much integrated due to life processes, so that the physical system retains less dominance than in the dawn of life.
    If life is seen as a response system, perhaps its function is to diminish entropy, and thereby increase order and complexity as described by Kauffman, not increase it.  But as I do not know if the overall results of entropy production in the ATP or photosynthesis systems are net positive or negative, which would give a clue, I can’t be sure. It is clear however that such processes in organisms create a very large amount of order, which no doubt diminishes entropy in the interim.  Self-organisation in a community or ecosystem could be in order to decrease entropy found in the physicochemical planetary environment, and this could be seen as a form of efficiency.
  In that type of scenario, organism death would be when the (body) system can no longer provide a response (literally) and when in fact entropy does increase. However this is simplistic because apostasis (cell death) appears to be some sort of necessary component of bodily systems so that cell growth (cancer) can actually cause illness and death. My final thought on this is that when watching the lion killing the buffalo, I can’t see how other than with trophic energy explanations (which was an important addition above) anyone can see too much order in that. Therefore if such a process as death is the reverse of order, it may be the mechanism to ensure that ultimately ecosystems obey thermodynamics and produce net entropy.

not an information paradox

I suppose I should be grateful because a theory has been put forward that resolves the information paradox, involving materials that only collapse down to a certain point and then are released along with the information to the universe eventually.  This is called bouncing.  Oh well, regardless of the name at least I am no longer required to be a hologram.

http://news.yahoo.com/paradox-solved-information-escape-black-hole-104543630.html

Holographic Principle and other concepts

I have removed my post on the singularity as I feel after watching some further docos/Utube I don’t have enough knowledge to properly comment, and will post it again when I am more sure of my facts.  However I am still not a supporter of the Holographic Principle which explains how 3D objects can disappear into Black Holes whilst being retained as a 2D image on the boundary of the singularity.  Thus in this serious scientific concept we are only holographs, possibly reflected off the edge of the Universe.  That seems to me to be wrong, so I suggested another mechanism to explain the apparent disappearance of information in a singularity.  But I now think I was jumping the gun without the required knowledge, so will add it again when I have more information.

Thanks for comment Harry but I am not commenting on the art side of things rather the scientific.  The Sci Am article was in the 1990s and showed differential equations with a hollow centre from memory, I will find it one day and post a link.  The interesting thing was that the equations extending concentrically from the centre showed highly ordered graphics, and also Nothing was at the centre, surrounded by some chaos.  As we now know, Nothing actually contains energy in which particles appear and disappear, and for some reason some matter was retained in the early Universe and not annihilated by antimatter as in a vacuum or Nothing, hence matter in the Universe became a possibility.

However not only matter becomes a possibility, but Order and complexity become possible if matter is not completely annihilated, although as known eventually even that succumbs to entropy.  Thus cells are organised into organs in highly ordered and complex structures, and molecules into amino acids into very complex proteins and enzymes.  The organism arises from virtually nothing into an immensely complex superorganism containing trillions of bacteria and many organs providing different functions.  However at the same time cell apostasis occurs so that many cells die throughout a lifetime, and there is an entropic end to all that order and complexity as life declines and ends.

Perhaps the Universe is beautiful in many ways, but it is also hugely destructive, hence we have destructive singularities and the predator/prey conundrum; in the empty vacuum matter is created and immediately destroyed; and life is born but later ceases.   Nature is not just pretty nor purely creative, but if you have noticed the most destructive predators are also some of the most beautiful, which is, as a biologist rather than physicist, a paradox that I find interesting.  Please see image of kitty on this site for instance.  I feel that Einstein showed the creation of matter, but there needs to be a formula for its demise, because there always seems to be exponential or another type of decline, including in massive bodies like the Sun, so that all matter conforms to the entropy principle, regardless of the level of complexity it has reached.

As a biologist I sometimes think that physics theories seem a little “out there”, and one of these is the Holographic Principle, by which we are not real 3D bodies, but images, enabling only 2D information to be retained at the boundary of the singularity.  I also think that the Multiverse is likely to turn out to be a series of probabilities, by which many universes could have come into being, however ours was the one that did as it has a remarkable set of required parameters to do so.

I sometimes wish Astrophysicists would come down to Earth a little.  I know the Universe is full of unexplainable and extraordinary phenomena, of which Life is decidedly one, but I still feel more logic needs to come into the explanations.    For example it seems  obvious from recent evidence that seems to indicate our Universe fits the “flat” model in which it is infinite, rather than having boundaries.  How does one have a reflection off an edge of the universe that is not there, if that is how the holographs are formed?  How also does one have multiple universes as ours is infinite so leaves no room?  Perhaps mathematically it is possible to have multiple infinities for multiple universes- otherwise where is the logic?

I do not think that Time is real however in the sense of being a separate dimension, I think it is a derivative of 3D, that is, it equates to change in form, so that it still real, but a derived property.  However again my maths is not too good with that and I imagine if I trawled thru Utube I would find mathematical proof that Time exists as a separate dimension.   I am not particularly skilled in the higher maths that is required to understand astrophysics, although increasing it is being required for ecological theories, so I may have to improve there.  But it seems to me although the maths is obviously highly sophisticated, the logic sometimes seems to be missing!

It thus seems logical to me from a number of angles that 3D Life, and other bodies, are decidedly real rather than holographic images.  If the latter were true, what arose from nothing was not matter and antimatter but image and anti-image which seems to me unrealistic, as we know that matter does indeed derive from energy from Einstein, and there seems little evidence it is not real and 3D.  Therefore…find other explanation…. for the disappearance of 3D information in black holes!

However I do have to qualify my rather speculative posts on the basis of not knowing enough of the maths or the physics required, to understand the sophistication of some of these theories, even if the logic seems to have gone completely AWOL!  Is this a logical or an illogical Universe?  To my mind it is a supremely logical one, which is exemplified by the mathematical fluidity of it, so that some think it is a mathematical Universe, and that matter etc. flow on from that.  I think this is partially correct.

However if surmising that illogical things exist such as Holographic Life and Matter, does that lead to the premise that there are one or more illogical universes?  And that therefore the maths must be illogical?  This is probably getting a little philosophical.  However if 3D is in fact real, and matter is therefore real, rather than holographic, then it seems likely to me that the presence of form has an influence, so that although form conforms to mathematical concepts, it is not solely defined by it.  Therefore concepts such as a mathematical universe are to my mind only partially correct.

Until I get time to update my physics, I am going to leave my previous speculative post aside.

Beginning the blog

Starting a new blog so will take a bit of time to get it sorted. Welcome.