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Posts posted by jimmydasaint

  1. First of all, can you get pure samples of each genus?

    If you can get hold of pure samples then you can do some old fashioned protein SDS PAGE made against secreted antigens from each genus.  These are probably few enough so that you end up with a reasonable protein profile.  If you make radiolabelled antibodies against the secreted antigens, you have a fine control of the secreted proteome from each genus.

    Then you can use some fancy reverse genetics to make a DNA probe for each genus and then finally use your chosen method to identify genus/species specific DNA.  I am assuming that there is enough genetic difference to classify the cyanobacteria into distinct criteria.


    Distinct Differences in Repertoires of Low-Molecular-Mass Secreted Antigens of Mycobacterium aviumComplex and Mycobacterium tuberculosis



    Small secreted proteins enable biofilm development in the cyanobacterium Synechococcus elongatus

    15 April 2016
    03 August 2016
    Published online:
    25 August 2016


    Small proteins characterized by a double-glycine (GG) secretion motif, typical of secreted bacterial antibiotics, are encoded by the genomes of diverse cyanobacteria, but their functions have not been investigated to date. Using a biofilm-forming mutant of Synechococcus elongatus PCC 7942 and a mutational approach, we demonstrate the involvement of four small secreted proteins and their GG-secretion motifs in biofilm development. These proteins are denoted EbfG1-4 (enable biofilm formation with a GG-motif). Furthermore, the conserved cysteine of the peptidase domain of the Synpcc7942_1133 gene product (dubbed PteB for peptidase transporter essential for biofilm) is crucial for biofilm development and is required for efficient secretion of the GG-motif containing proteins. 


  2. 4 minutes ago, dimreepr said:

    So is the bible...

    You still don't need God, just the message.


    First of all best wishes for the New Year to you and your loved ones. Of course you are correct in saying that we don't need God to live in harmony. I think many people  would need a perfect archetype or paradigm against which they can measure the evolution of their Ego, Will, Love and Knowledge, so I referred to an absolute embodiment of personality and qualities in the form of God, rather than humanity, often painfully lacking in both.

    My aim was to present a picture of God in a scientific context. I don't know if I succeeded or failed in my efforts.



  3. My own tuppence worth as a believer for about 34 years now.

    Science is a set of techniques which can be used in a hypothesis/falsification/new hypothesis method to find objective truths.

    It is neutral to the existence or absence of God

    The Universe, as we know it, is either infinite or finite.

    If it is infinite then my whole argument falls apart.

    If it is finite, then it had a start.  That start is a hypothesis called The Big Bang.

    Science has given evidence of the existence of a Big Bang -for example, cosmic microwave background, Hubble red shift of galaxies 

    The Laws of physics apparently came into being at the Big Bang and then became pretty much immutable.

    Matter cannot be created or destroyed. God created matter and cannot be then contained or trapped by His Laws.

    Space-time was created by God. The Bible and other revelations spend time telling us what happens at the end of "Earth" time so God has seen all of Time as it passed before Him.

    God's revelations appeared in all three theist religions but as metaphor and allegory not in complete factual detail.  God gave a spark to the start of the Universe and let his revelations and Laws do the rest.  

    God gives meaning and purpose to the lives of billions of people on this planet, including myself.

    If you do not believe or seek a scientific proof for God, it is not there. What would be the point if we have something called free will if a Father like figure showed His presence all the time - it would be restrictive in the extreme.

    But if you are an atheist, I respect your views. 

    I love my belief system because it enables me to live with my Ego, Love, Will and Knowledge in a harmonious manner with other people and the Universe (most of the time, unless they really get irrational when I lose the plot slightly). In short, I have hope for the future if I align my moral compass with the intrinsic qualities and personality of God.  

  4. Quote

    From Prometheus - This seems to suggest you see inner peace as being the same as having no feeling?  Not sure if that is a reflection on Buddhism, but it is a common misinterpretation of the practice.

    For instance it's quite common amongst people new to meditation to think that they must clear their minds of all thoughts. But the brain is an organ that thinks - to try to stop is as foolhardy as trying to to start your heart from beating.

    My take on inner peace is that you lose your sense of self and separateness from the world. You don't feel like a dancer dancing, there is only dance. You don't feel like a footballer playing football, there is just the ebb and flow of the match. You don't feel like a monk sitting there clearing your mind of all thought, there is just wholehearted sitting. You don't feel like a husband having an argument with his wife, there is just the full blooded heat of the moment.

    None of your emotions or perceptions change, it's just that you relate to them in a different way.


    dimreepr, if this is what you are saying then I agree with it. Also, I think it is quite pleasing to "live in the moment" and to understand that feelings come from thoughts and our relationship to the thoughts we generate can change our perceptions of the world.   What I have achieved, through self discipline and from a hard life is a sense of calm and gratitude; maybe that is as close as I can come to inner peace but it is a subjective inner peace. 

  5. dimreepr, you appear to a guy who is my age group (50-55?).  Inner peace as you feel it seems to be easier with more age as you have passed the age of reproduction and searching for the ideal job etc... From looking at the last page of posting, I guess no-one has inner peace as an absolute, but they have moments of peace in their lives (IMO). 

    I just need some "me" time and I can confess to a feeling of peace.  A bit of meditation with intent and I feel close to peace. 

    But, when I am knackered at the end of a long working day, fraught with troubles, and return home to a traffic jam of epic biblical exodus proportions, it is OK to let off some steam and then return to peace later.  We are only human my friend; imperfections make us human (if I remember my first series of Star Trek as a youth). 

  6. As the Benedict's Test is for monosaccharides and maltose ( a disaccharide), I would have thought that heat would be needed to thermodynamically favour the linear form of the sugar which is able to reduce the Cu++ ion in the Benedict's reagent to Cu+ causing the colour change from blue to brick-red. The mechanism seems to be as follows (with the sugar in the aldose form instead of the ring form and then oxidised into a carboxylic acid with the simultaneous reduction of Cu++ to Cu+)):



    If it is true that heat is needed to open up the closed ring structure of monosaccharides, the reaction might not take place at room temperature. I am not sure about this point. 

    Image result for ring and straight chain structures of glucose


  7. beecee, I think that this comment gets to the heart of what the scientists are trying to do at what can be considered "low" energies in comparison to the energies used in the LHC (50-7-MeV IIRC):


    One of the consequences of a noncommutative spacetime is that there are no singularities, which has implications for other areas of cosmology, such as the big bang and black holes.

    With their proposed test, the physicists' goal is to find experimental evidence supporting the idea that spacetime does indeed have a noncommutative structure. To do this, the proposed test attempts to detect any changes in the conventional commutative relations occurring in a micromechanical oscillator. If these changes are present, they would indicate a noncommutative structure and produce a measurable optical phase shift on a light pulse that has been coupled to the oscillator.

    Using current optical setups, this phase shift can be measured with sufficiently high levels of accuracy that, according to the physicists' calculations, would make it possible to access the energy scale near the Planck length. By accessing this scale, the experiment could potentially probe the effects of noncommutative theories at the energy regime relevant to quantum gravity.

    Read more at: https://phys.org/news/2017-10-physicists-quantum-gravity-current-technology.html#jCp

    For people who need a simple explanation of non commutativity, I highly recommend the following:


    The following is a phase shift from an oscillator: 

    from THz oscillator.  Physics bods, help us out with an explanation of the proposed new experiments....


  8. Thanks for that info Strange.  I am now going to try and summarise, from a layman's point of view, the Classical Model of physics using an explanatory diagram:


    Credit : https://creativecommons.org/licenses/by-sa/3.0/


    From my limited viewpoint, the Classical Model uses the theories of Newton, Maxwell and Einstein but does not provide a link between behaviour at large scales (e.g. stars, planets, humans) and at an atomic/subatomic (quantum) scale. Quantum mechanic theories (e.g. string theory) do not lend themselves to experimentation normally but this experiment may be able to explain something about gravity at quantum scales without using energy at higher scales than the Large Hadron Collider.  Right so far? If so, let's consider the simplified version of the paper supplied by Strange...


  9. 2 hours ago, koti said:

    I do too. As for replacing hate by love I find it peculiar to say the least. I need my hate as much as I need my love and all other emotions - they make me who I am. Obtaining a constant state of contentment would erase my identity as a person. 

    I haven't actually achieved a Nirvana-like state yet.  However, I don't feel hate or envy with any intensity.  It might just be just an age effect but I do feel a lot calmer much of the time.  If I could achieve contentment with what I have, I would love to have that feeling. I think inner peace means a " homeostasis" of emotions with emotions still present in the psyche but without the swings - just my opinions for what they are worth. 

  10. 7 hours ago, koti said:

    When I hold my 18 month old in my arms I feel the same but I presume that both the mental and physical reactions of my body in that state are love not inner peace. I guess.

    Love and peace go hand in hand surely. When you love something absolutely, do you not receive a feeling of inner peace? I do.  

    I suppose that if you are able to replace hate by love, or be calm in the face of adversity as StringyJ mentioned, that is pretty close to achieving inner peace.  I think that the calming of thoughts is a good start.  I have not always been successful, as past confrontations with trolls will testify, but at least I try....

  11. It is certainly a bloody good ghost story.  The missing concerto was known about by a number of Schumann's relatives and others, who may have sought a way to bring it to light again.  I heard it on BBC Radio 3 a few days ago and it is magnificent as a musical piece. However, I will just have to stick to relying on out of body experiences as an analogue to death and see if evidence can come to light about a "soul" floating up towards the ceiling. 

  12. Why choose to inhibit LH?  There is an alternative. The body can be flooded by an LH analogue that binds to LH receptors and therefore causes downregulation of LH.  It is an easier option than directly targetting LH or GnRH. This would stop ovulation but allow the rest of the cycle to take place IMO.  The truth is that I don't know and am making an educated hypothesis.

  13. Schumann, the composer, died and left a violin concerto behind.  During a Ouija board session, he apparently asked for his missing concerto to be found and played.  This took place but many decades after it was "lost" and then put into storage. Is the story fake? Or is it coincidence?


    A concerto rises from the dead in 'Ghost Variations

    A lost Robert Schumann masterpiece, which was rediscovered  in the 1930s thanks to messages from a Ouija board, inspired  Jessica Duchen’s extraordinary new book

    schumann-hulton-getty.jpg Schumann's Violin Concerto, his last orchestral work, has had a chequered existence (Hulton Archive/Getty Images)


    When I first heard the story of how Robert Schumann’s Violin Concerto came to light in the 1930s, I nearly fell off my chair.

    This extraordinary piece, the composer’s last orchestral work, has had a chequered existence. After one airing by its intended soloist, Joseph Joachim, it languished in obscurity for nearly eight decades. Then in 1933 Joachim’s great-niece, the Hungarian violinist Jelly d’Arányi (one-time muse to Bartók, Ravel and even Elgar) claimed to have received spirit messages via a Ouija board begging her to find and perform it.

    So bizarre was her quest – extending to the highest echelons of the Third Reich’s administration – that I’ve turned it into a novel, entitled Ghost Variations. The book has been taken up by the groundbreaking publisher Unbound and is due out this summer.

    The violinist Jelly d’Aranyi, once a muse for Bartók and Ravel (Hulton Archive/Getty)

    The reality is admittedly stranger than fiction. After Schumann’s death, his widow, Clara, put the concerto aside, fearing it might betray its composer’s increasingly unstable state of mind. Always prone to extreme highs and lows, Schumann may have been bipolar, or suffered from tertiary syphilis, or possibly both; academics remain divided on the nature of his malady, though most incline towards the syphilis explanation. In February 1854 he suffered a devastating breakdown and tried to drown himself in the Rhine. Having survived, he requested to go into a mental hospital. He spent his final two years in an asylum in Endenich, Bonn, and died there in July 1856.

    Thereafter, it was up to Clara to decide which of her husband’s unpublished works should see the light of day. In consultation with her two right-hand men, Johannes Brahms and Joachim, she took time to make up her mind about the concerto. Finally she elected not to issue it. Joachim’s heirs deposited the manuscript in the Prussian State Library, placing what was thought to be a 100-year embargo on the work. Schumann’s daughter, Eugenie, insisted that in fact her mother wished it never to be played.

    Jelly d’Arányi was 14 when her great-uncle Joachim died. Her elder sister, Adila Fachiri, likewise a celebrated violinist, had been Joachim’s pupil in Berlin. Fachiri was, as it turned out, a psychic “sensitive”, able to receive at considerable speed and intensity detailed “messages” in the then-fashionable Glass Game (ie, a home-made Ouija board).

    Although d’Arányi herself claimed to have received the initial message, she rarely participated in such sessions. It was largely Fachiri and her friend Baron Erik Palmstierna, the Swedish Minister in London, who drove the search thereafter; Palmstierna himself unearthed the manuscript in Berlin; and his book Horizons of Immortality, based on “messages” interpreted by Fachiri, broke the news of the concerto’s revelation upon an incredulous and cynical public in September 1937.

    Full Story

  14. When I hold my baby grand daughter in my arms, I feel a calming of the ocean of my thoughts which reflects and affects the calmness of my body.  I guess inner peace is a lack of thousands of thoughts racing through the mind.  Something the Dalai Lama probably experiences...

  15. Nice find doc, although you gave away the plot in the O.P. In fact there are also doubts that the teeth belong to a hominin at all.  In the same article, it was noted:


    Sergio Almécija, an anthropologist at George Washington University who also studies pliopithecoids, agrees. As for the supposedly hominin-like canine, the experts’ opinions range from interest to dismissal. Begun even doubts that it's a canine.

    “The 'canine' looks to me like a piece of a ruminant tooth,” Begun says by email. Ruminants are cud-chewing, plant-eating mammals such as cows and sheep. “It has a funny break that makes it look a bit like a canine, but it is definitely not a canine, nor is it [from] a primate.”


  16. Found the explanation for gold. Electrons around the nucleus are in probabilistic shells. https://chem.libretexts.org/Under_Construction/Textmaps_and_Wikitexts/MVC%3A_Chem_1406/Chapters/02._Atomic_Structure/2.5%3A_Arrangement_of_Electron_(Shell_Model)

    Electrons can absorb energy from light and "jump" from one shell to a higher energy shell.  They absorb at different frequencies for silver and gold.  Silver s-shell electrons absorb light in the ultraviolet end of the light spectrum and reflect all the other colours evenly giving silver  that silvery metal colour. 

    Gold has s-shell electrons attracted with by an intense, 79 + charges from the nucleus.  As a consequence, the electrons  in gold following Einstein's relativistic principles, because, IIRC, the electrons gain speed/ angular momentum to avoid the attractive forces from the nucleus and also gain mass. The angular momentum orbit radius decreases.  The light absorbed by the electrons is in the blue part of visible light, as opposed to the ultraviolet end of the light spectrum so that the remaining colours combine to give a yellow gold glitter. 


    Please correct as appropriate. 

  17. Point out mistakes  as much as possible, as long as you cite evidence. Just don't patronise a Scotsman, we don't take this well. I was not attacking Memammal.  I thought he made a mistake .  This theory is decades old - I presented the evidence using the References. Let's go forward by referring to the paper and I will show my openness and intellectual honesty in admitting my errors. Both of us should read the paper first and make comments later. 

    From my brief reading of the paper, I can back up Memammal's conclusions that larger functional ligases occur from the smaller ligases. However, the researchers admit that the efficiency is low. 


     Conclusion: implications for RNA evolution at the origin of life

    Ligases (and related polymerases) have primarily been explored with the aim of evolving a self-replicating enzyme (2).  The results indicate that, in the early stages of the RNA world, molecular size could have increased in a modular, stepwise fashion via the reactions of small ligases with a range of oligomers, albeit with a relatively poor efficiency. It supports the computational and theoretical predictions that assembly of larger functional molecules resulted from short RNA ligases [26,27]. The derived larger and more complex ligases developed specificity and efficiency for the kinds of substrates ligated. This trade-off could have contributed to building molecular complexity and the generation of a pool of functionally specialized molecules, which were necessary for the emergence of a self-sustained replicating system.

    was small.  Earlier,the same researchers asserted the following statement: 


    The largest ribozyme, R18, self-ligated only 7 out of 24 different substrates and was most selective in its function. and also: " With increased molecular size in larger ribozymes, the degree of folding and self-pairing increased (as determined by the Gibbs free energy: R18-T4 (−3 kcal mol−1), R18-T3 (−18 kcal mol−1), R18-T2 (−31.2 kcal mol−1), R18-T1 (−46.7 kcal mol−1), R18 (−67.3 kcal mol−1))".


    Previously, other researchers have had to address the following issues raised by other scientists:: 


    However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as ‘proteins first’, which holds that proteins either preceded RNA in evolution, or – at the very least – that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.


  18. On 25/09/2017 at 0:16 PM, Area54 said:

    Hi Jimmy,

    I am a bit puzzled by your post. Which part of " Their results are published today in the journal Royal Society OS, in a paper entitled "Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life” did you not understand. (i.e. it is current and it is in a journal.) The published article, in the Royal Society's open access can be accessed here.

    That said, I'm still studying the article to determine what they think they are saying is new. In that regard I share your puzzlement.

    Don't be so patronising and sarcastic.  Try to be positive and helpful instead of displaying your arrogance.  I hope that your summary of the article will show knowledge instead of sneering at people.

    To help things along let's examine some evidence.  The bibliography section will inform all of us about the date of the theory:


    References  ↵Gilbert W. 1986 Origin of life: the RNA world. Nature 319, 618. (doi:10.1038/319618a0)CrossRefGoogle Scholar ↵Joyce GF. 2007 Forty years of in vitro evolution. Angew. Chem. 46, 6420–6436. (doi:10.1002/anie.200701369)CrossRefPubMedWeb of ScienceGoogle Scholar


  19. I get your point about batteries, and agree that it is a sensible way forward, but recharging them would still need the high energy provided from fossil fuel power stations, IMO. I tried to find a comparison of energy outputs from fossil fuel burning and "cleaner" sources but could not find the info in ten minutes of searching. I did find this though:

    Fossil Fuel Heat Content Renewable 
    Heat Content
    (non-renewable) kJ g-1 MJ tonne-1 kJ g-1 MJ tonne-1
    natural gas 54 54 000      
    petrol (gasoline) 48 48 000 E10 (gasohol) 44 44 000
    diesel 45 45 000 biodiesel 42 42 000
    black coal 34 34 000 bioethanol 30 30 000
    brown coal 16 16 000 biogas 26 26 000


    It is a pity that I couldn't find direct efficiencies for each fuel but fossil fuels kick ass for energy output compared to other sources. 

  20. I was thinking about the efficiency of solar panels and unpredictable wind energy to power towns and cities, rather than solar powered cars. 


    DS1's solar panels convert 22% of their available energy into electrical power. This may not sound very good, but it is much better than most solar panels. Most solar panels on people's houses, for example, are fairly inefficient. Less than 14% of the energy that reaches them will be converted to electricity.


    In regard to cars, I am considering that the cars would be using sources of power that can be renewed from non-fossil fuel sources, like the batteries you mentioned. 

  21. On 17/09/2017 at 1:04 PM, StringJunky said:

    Thinking about it , if China gets the lead on this, the US, Russia and the Middle East are possibly going to see quite a power shift away from them through the shift in energy sources. Energy is a critical currency. I can't see that being a bad thing, even though China is communist.

    In my opinion, SJ, China have undergone an Industrial revolution similar to ours a few hundred years ago and are moving on to "post-Industrial Revolution days".  I anticipate that they will lead the world in non-fossil technology and make it more accessible for countries that they border, causing a new revolution in non-fossil fuel power. Any country that can raise 640 million people out of poverty deserve to be noticed.  They seem to be a complex capitalist/socialist society rather than Communist, and good luck to them! However, my question would be: is the energy too dilute to be useful to bring electricity to large towns? Do we all have to significantly change our lifestyles to accommodate a low fossil-fuel future? I am cynical, and hope I am wrong....

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