tag:blogger.com,1999:blog-7701411.post2997806935132549047..comments2023-09-28T21:40:05.328+10:00Comments on Dr Clam's accidental blog: ...then cry "Havoc!" and let loose the dogs of PhilosophyMarco Parigihttp://www.blogger.com/profile/00702055111711651319noreply@blogger.comBlogger24125tag:blogger.com,1999:blog-7701411.post-29259262157444576842012-01-17T13:03:55.781+11:002012-01-17T13:03:55.781+11:00I found this great quote from a random person in t...I found this great quote from a random person in the interwebz: <br />"I felt real anger and indignation when the definition of ‘universe’ was changed (arbitrarily in my opinion) from ‘everything that exists’ to ‘everything that exists within our segment of space-time’. To me this was intellectual laziness on the part of the astrophysicists who didn’t want to have to say that the ‘universe’ didn’t necessarily begin at the big bang but rather the portion of the universe that we exist in and the only portion that we currently have the ability to observe began at the big bang." (http://stuckinhyperspace.tumblr.com/post/2405799370/my-religion)Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-3886187087708271852012-01-13T11:20:51.673+11:002012-01-13T11:20:51.673+11:00Yes. It is. Ever since I read one of your Asimov b...Yes. It is. Ever since I read one of your Asimov books on science, I felt this chiral chemistry bizzo was of absolute dreadful importance in the "physical chemistry" part of the origin of life, even though I couldn't quite put my finger on exactly what it means. My first guess was that the weak force must in some way be the energy source for the synthesising metabolism that I kind of described in terms of solely physical chemistry component reactions. It's not metabolism as we know it. The "inside" is the complex molecule itself. Energy transfers are radiative rather than selective chemistry going through membranes - you get the drift - This is just the Guess/hunch part of science, which is the most important. However, I need to structure my hunch in a way that is testable - which will take some doing.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-38167596827954841082012-01-13T09:30:30.351+11:002012-01-13T09:30:30.351+11:00...something something Asimov something something ...<i>...something something Asimov something something radioactive decay something something left hand molecules something something why not 50-50 left and right something something donkey.</i><br /><br />Is <a href="http://aps.arxiv.org/ftp/arxiv/papers/1007/1007.3352.pdf" rel="nofollow">this</a> the kind of thing you are looking for?Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-53793940907115600742012-01-13T08:07:44.808+11:002012-01-13T08:07:44.808+11:00I guess what I am trying to say is that in a &quo...I guess what I am trying to say is that in a "physical chemistry" sense, reproduction looks a lot like catalysis. And it wouldn't even matter if the mass production of a relatively complex molecule was just due to the nature of the conditions. My assumption is that nature builds on complexity only if natural selection can be made to bear on it- even if is nothing like natural selection as we know it. Clearly, in a physical chemical sense, self catalysis, or a cycle of catalysis is the only way that "inheritance" can come into it. Whether, as you say, the reactions wouldn't happen that way in space, and the source of energy might be something like geothermal underwater chemistry or whatever. But I strongly believe the building blocks of DNA would have to evolve, but in a completely different way than how it does that now, and in an environment common pre-earth.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-24839606360448262692012-01-13T07:42:25.044+11:002012-01-13T07:42:25.044+11:00Plausible explanation: The meteorites are remnants...Plausible explanation: The meteorites are remnants of the original molecular cloud from which the solar system condensed, in which hydrogen cyanide, ammonia, and water were generally distributed, and hence nucleobases ended up being generally distributed too.<br /><br /><i>In the lab, an identical suite of nucleobases and nucleobase analogs were generated in non-biological chemical reactions containing hydrogen cyanide, ammonia, and water.</i>Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-80426792913920896632012-01-12T20:32:09.554+11:002012-01-12T20:32:09.554+11:00Is there a plausible explanation for them to be on...Is there a plausible explanation for them to be on all the meteorites?Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-30177397696072529682012-01-12T19:37:42.071+11:002012-01-12T19:37:42.071+11:00From what you sort of were telling me, if some nuc...<i>From what you sort of were telling me, if some nucleobases were in the mix, they would catalyze reactions that would generate more nucleobases of some kind.</i><br /><br />Er, no. This is what you sort of told me, and I have been saying isn't going to happen...Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-26825700151033056662012-01-12T19:33:25.351+11:002012-01-12T19:33:25.351+11:00Oh. And if this is found to be a supremely primiti...Oh. And if this is found to be a supremely primitive form of reproduction, the supremely primitive metabolism, is the energy exchanges which enable the molecules to reproduce.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-46445451827435084402012-01-12T19:29:15.718+11:002012-01-12T19:29:15.718+11:00I am a little confused just trying to piece togeth...I am a little confused just trying to piece together the latest NASA discovery of neucleobases on all the meteorites they tested. This is measured in parts per billion, but compared to the places they landed, that is high enough and of the type that would indicate that they originated from the parent asteroids they came from. This matches another study which indicates that the chemistry of a lot of asteroids including cyanide, water and ammonia, could very plausibly have generated these bases. From what you sort of were telling me, if some neucleobases were in the mix, they would catalyze reactions that would generate more neucleobases of some kind. Thus I'm surmising, that if a chunk of asteroid from a collision, landed on another asteroid, bringing some neucleobases with it, that it would "seed" the virgin asteroid, catalysing the formation of neucleobases that may not have otherwise formed. Let us just consider this part of the puzzle first. If this is what happened, are they "reproducing?. Now if they survived on a relatively small chunk of asteroid subject to sporadic ionizing radiation, and were still in a chemical form that could "seed" other systems to catalyze their reaction, while other candidate molecules wouldn't, would that make them more likely to catalyze the reactions that they catalyze, than other reactions ? Would this not be a rudimentary form of selection? If the end product of the reaction they catalyse is also a nucleotide base, would that not be a form of inheritance? I'm not playing semantics here, and Ithe next step is not going to be of the exact nature of this step, but is this very,very, very basic selection and inheritance.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-66963845808147625342012-01-12T13:54:12.143+11:002012-01-12T13:54:12.143+11:00Okay, let me rephrase that: 'I think anything ...Okay, let me rephrase that: <i>'I think <b>anything containing nucleobases remotely susceptible to inheritance and selection</b> would have happened a long way along the process of 'protobiotic evolution' in a system that was already complicated and delicate.'</i><br /><br />Complicated and delicate meaning it has to not be in an environment bombarded by radiation, but down in the sea-bottom mud on a planet or deep in the interior of a big dirty snowball. <br /><br />'Subject to selection and inheritance in a very basic way' presupposes sugars and phosphates and reactions that would produce them all as intermediates and a way to separate the 'system' from the 'surroundings' - in fact, all the interesting things that we want to explain. Replication is not something that happens with nucleobases by themselves. To paraphrase something I said long ago: looking at nucleic acids and proteins and trying to work out the origin of life is like looking at smartphones and sattelites and trying to work out the invention of the telegraph. You can't get there from here!Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-30861669519114167592012-01-12T10:56:42.505+11:002012-01-12T10:56:42.505+11:00ATP and GTP are similar chemically to the neucleot...ATP and GTP are similar chemically to the neucleotide bases, and they are used for energy in all sorts of ways within living cells. Before there was something complex and delicate (which I assume involves membranes of the type you talk about in your metabolism posts) I am postulating there was something less complex and hardy to hostile environments including radiation, and capable of using all sorts of energy (from a sun, or from radioactive decay of some elements)to the sole purpose of powering the generation of the building blocks of neucleic chemistry, including energising the future energy currency. I am postulating that these building blocks were subject to selection and inheritance in a very basic way, that in the environment of colliding asteroids of various sizes with fairly high radiation,there was a survival of the fittest happening. Thus whereas the elements concerned may have been expected to form random combinations of molecules, a large chunk of them formed these bases and are spread through all the asteroids in varying concentrations. Once you have the assumption of high concentrations of this soup of bases, then you can look at how these could be polymerised into more complex compounds, that could separately be subject to reproduction and rudimentary metabolism, selection, mutation and inheritance.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-56703778427365895362012-01-12T08:21:11.989+11:002012-01-12T08:21:11.989+11:00Ok. So I get that the endpoint we are getting towa...Ok. So I get that the endpoint we are getting towards is nucleic acid. But I do want to explore whether some forms of catalysis are like reproduction. Ie. if seeded with a base, does this multiply the number of bases you end up with? And can this reproduction be "powered" ie, energy is absorbed and catalyses the process, but then excess heat just radiates away, doesn't reverse the process. Can this plausibly match your energy graph for metabolism? Also, as far as I understand, chemical bases are recycled more than created within the nucleus, so for more complex chains to evolve a requirement is a high population of bases.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-65445816082245053752012-01-12T07:53:53.849+11:002012-01-12T07:53:53.849+11:00That's not metabolism, that's just catalys...That's not metabolism, that's just catalysis. In segueing from nucleic acids to nucleobases you have lost the nugget of gold in your original hunch. <br /><br />Like I said: <i>...There is very likely to be a connection between the adoption of DNA and metabolism, since ATP and GTP are 'energy currency' in living systems - but I think the adaptation of a metabolic process to reproduction would have happened a long way along the process of 'protobiotic evolution' in a system that was already complicated and delicate</i>Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-11457723617083169812012-01-11T17:36:25.449+11:002012-01-11T17:36:25.449+11:00From.
http://www.nasa.gov/topics/solarsystem/feat...From.<br /><br />http://www.nasa.gov/topics/solarsystem/features/dna-meteorites.html<br /><br /><br /> <i>"In the lab, an identical suite of nucleobases and nucleobase analogs were generated in non-biological chemical reactions containing hydrogen cyanide, ammonia, and water. This provides a plausible mechanism for their synthesis in the asteroid parent bodies, and supports the notion that they are extraterrestrial," says Callahan.<br /></i><br /><br />I wish I knew a chemist somewhere, that would set up an experiment for his honours students, to demonstrate that these neucleotides use a rudimentary "metabolism", using energy to reproduce themselves in conditions like on an asteroid...Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-26637930212264597242012-01-11T17:20:09.368+11:002012-01-11T17:20:09.368+11:00Woohoo. Look what I found casually looking for inf...Woohoo. Look what I found casually looking for information about the chemistry of neucleotides!!!! From Wikipedia: Neucleotides<br /><br /><i>In August 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting nucleobases (such as adenine, guanine, xanthine, hypoxanthine, purine, 2,6-diaminopurine, and 6,8-diaminopurine) may have been formed extraterrestrially in outer space.</i><br /><br />This is looking closer and closer to the origin of metabolism/life. Outer space.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-14978866541401966602012-01-11T12:11:20.651+11:002012-01-11T12:11:20.651+11:00I am not sure of the "endpoint" of evolu...I am not sure of the "endpoint" of evolution I am trying to get to here, but in subjective terms, I am looking for an environment and system whereby the building blocks upon which DNA is built on are "reproducing". In this sense I am looking at the neucleotides and related molecules. I am trying to think of an environment ( possibly a common environment in the stretch of space that predates our solar system) where an energy source applied to a molecule (neucleotide like) would cause neighbouring molecules to arrange themselves into a neucleotide without destroying the original neucleotide and when that is complete, the process would repeat with both neucleotide type molecules. The environment in which this happens would of course be completely different to the environment for the next step, which would, however require an abundance of neucleotide bases being available from the previous step. This process should be still apparent somewhere in the galaxy, or be able to be simulated from what we know about the pre-sol era in this stretch of space.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-5204340826022054052012-01-11T10:02:17.274+11:002012-01-11T10:02:17.274+11:00Re Facebook, nobody read my stuff there either. Th...Re Facebook, nobody read my stuff there either. The "Global Warming Is a Myth" essay was up there for years with no comments :(Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-23779166961797382392012-01-11T07:38:31.965+11:002012-01-11T07:38:31.965+11:00You got me interested even though I have absolutel...<i>You got me interested even though I have absolutely no information on what the argument was about.</i><br /><br />I'm not sure which argument you are talking about here?<br /><br /><i>I wondered if you know of any sources of information about the physical chemical properties of dna (principally mitochondrial dna)...</i><br /><br />I'm glad you like the 'Show me the Metabolism' posts :D I haven't had a look yet for information on the properties of DNA but I expect you can do as well as I hunting facts in cyberspace. I think you are on to something in that there is very likely to be a connection between the adoption of DNA and metabolism, since ATP and GTP are 'energy currency' in living systems - but I think the adaptation of a metabolic process to reproduction would have happened a long way along the process of 'protobiotic evolution' in a system that was already complicated and delicate and (therefore) existing in an environment shielded from ionising radiation.Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-47488395335162096392012-01-10T12:21:26.687+11:002012-01-10T12:21:26.687+11:00...something something Asimov something something ......something something Asimov something something radioactive decay something something left hand molecules something something why not 50-50 left and right something something donkey.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-22452559625905463222012-01-10T12:07:41.376+11:002012-01-10T12:07:41.376+11:00Oh. By the way - I reread that absolutely excellen...Oh. By the way - I reread that absolutely excellent trio of posts about show me the metabolism. I have had this hunch swirling around in the back of my mind about how metabolism and reproduction co-evolved. The basis of my hunch is based on what dna is like and that what it is like can tell you about where it originated. A bit like the slit in a human zygote (embryo?) can lead you to believe that we evolved from creatures that had gills knowing nothing else. <br />I wondered if you know of any sources of information about the physical chemical properties of dna (principally mitochondrial dna) and in particular the energy transfers within the chemical structure when subjected to sporadic high level radiation doses. My hunch is that the dna acted both as a store of energy *AND* a store of genetic information in its raw form. The source of energy would be the strong ionising radiation, which would be stored in the chemical bases of the dna, and when shielded from the radiation would use this energy to assemble its helical or even substructures relevant to the organic molecules involved.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-17885011085186917322012-01-10T11:42:55.580+11:002012-01-10T11:42:55.580+11:00Indeed. You got me interested even though I have a...Indeed. You got me interested even though I have absolutely no information on what the argument was about.<br /><br />As for empathy - I have decided that it is entirely unnecessary on FaceBook. It appears just like a blog that more of your friends would actually read. It is still irritating that the most mundane of things go viral, and really amazing stuff gets ignored.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-59053576094323319972012-01-09T09:40:46.049+11:002012-01-09T09:40:46.049+11:00I guess as far as Lennox's treatment of Galile...I guess as far as Lennox's treatment of Galileo goes, I am with Nathanael (I presume) in asserting that there is no significant misrepresentation there. I also don't see any great interest or benefit in arguing about it.<br /><br />So far as the second thread goes... as you know... I am with you 102%.<br /><br />It is probably cowardice keeping me away from FaceBook. Cowardice, and a lack of human empathy manifesting as irritability. (Speaking of cowardice, I still haven't sent that email to start that argument I asked you about in Twitter.)Dr Clamhttps://www.blogger.com/profile/14985493422534275997noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-27491068330552440292012-01-08T19:10:33.225+11:002012-01-08T19:10:33.225+11:00I don't understand what your objection to Face...I don't understand what your objection to FaceBook is, it would really be good to have you there, even if you block absolutely everything you object about it.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.comtag:blogger.com,1999:blog-7701411.post-48058965676630903572012-01-08T19:08:22.847+11:002012-01-08T19:08:22.847+11:00Well to answer the first sentence. Nathanael read ...Well to answer the first sentence. Nathanael read this book a while back, and agrees with it in general. His brother Winston Inabox has been convinced to read it, and although he hates it is reviewing it for discussion on his Facebook wall as he goes. I have worked out how to "cut and paste" roughly by taking a screenshot of the relevant pages. At this stage there has been a thread on Galileo, where me and Winston more or less agree that Lennox had somewhat misrepresented what actually happened in relation to the conflict of church and science. The second thread is regarding the requirement of faith in science. I believe there is a requirement for faith, and that it is the New Atheists that are misrepresenting this requirement, while Winston is adamant that it is Lennox playing semantics.Marco Parigihttps://www.blogger.com/profile/00702055111711651319noreply@blogger.com