Louis
Posts: 6436
Joined: Jan. 2006
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RedDot,
1) | Quote | | First, if my terms are not relevant, can you please identify for me what is the smallest protein that naturally exists in a living organism? (And dont throw in some peptide like a-corticotropin either). Or for that matter, what is the largest protein that natually exists in a living organism? I'll need that information to develop this discussion further. |
No, you need that data to keep perpetuating the straw men you have erected. Look at the things Wesley has supplied (thanks Wes), and do your own research. I'm getting the distinct impression that your knowledge and understanding of chemistry is not what you think it is.
You are also making a (false) distinction between a polypeptide and a protein on a (misunderstood) molecular basis. More on this further down. The straw man you repeatedly make is that some minimum **modern** protein/organism must be the first replicator.
2) | Quote | | Kinda puts a kink in that whole "no one is claiming or has claimed..." bit. If you'd like I can whip out something from Dawkins. |
Carry on like this RedDot and I am going to become annoyed with you. The key word is MODERN. Kary Mullis thinks that abiogenesis happened, great! Big news! So do I and hundreds of thousands of other scientists in the relevant fields. Incidentally Prof Mullis was wrong that memes and genes are the only replicators, but then he was speaking very generally. Nice try at quote mining. So no, it doesn't put a kink in anything I've said, or any actual scientific claims about abiogenesis.
3) As for the stuff about proteins, crystals and what not, sorry RedDot but you are so confused that it borders on the unintelligeble.
Are you saying proteins can't completely crystallise? If so, I'm sure it's news to Max Perutz and Sir John Cowdry Kendrew who got the 1958 Nobel Prize in Chemistry for their crystallisation and crystal structure of sperm whale myoglobin. I'm also sure it's news to the hoardes of crystallographers and medicinal chemists in the pharmaceutical industry who crystallise proteins and coc-yrstallise proteins with the drug targets to get better information about binding motifs and information for molecular modelling etc.
Are you trying to use crystallisation and crystals as an example of the "unusual" properties of macromolecules? I sincerely hope not. Crystals=/=macromolecules.
Are you simply saying that the crystallisation of biological macromolecules and polymers has it's own wonderous difficulties? If so, well done, it does, so what? The fact that they CAN crystallise shows that, again it is a physical phenomenon, no need for magic pixies or mystical deities.
The stuff about polypeptides not being able to be denatured gives me my final clue. You are utterly ignorant of basic chemistry and are merely reguritating material from some source you clearly don't understand. A protein is a polypeptide. Polypeptide refers to the multiple amide (peptide) bonds in the polymer. Take any polypeptide of suitable primary structure (sequence of amino acids that it is comprised of) and it will form, in solution and in solid state, alpha helicies, b sheets, gamma turns and so on and so forth, i.e. secondary structure. It will also in turn fold to produce a stable hydrogen bonded tertiary structure. That secondary and tertiary structure in any polypeptide is alterable by pH, temperature etc. That's precisely what denaturation is!
A protein is a specific polypeptide in a specific biological context, that's it. When one denatures a protein sufficiently one alters it's function in that biological context, depending on the severity of denaturation sometimes to the point on loss of function. That, for example, the structure of human PPAR gamma is not the same in solution as it is in the solid state or that if you synthesised the primary structure of human PPAR gamma that it wouldn't fold into the secondary and tertiary structure of natural PPAR gamma (unless you subjected it to the same conditions it has in vivo), is totally irrelevant. The secondary and tertiary structures of any polypeptide are alterable by pH and temperature. This false distinction between proteins and polypeptides you repeated make betrays your gross lack of understanding.
Don't bother reading those papers I provided, you simply don't have the basic knowledge required to understand them. Go back to a basic chemistry text and start from there.
4) Polypeptide synthesis. Again we see massive confusion on your part. The plethora of possible protein structures has no influence on their ease of synthesis. Yet you appeal to the "difficulty" again. The "difficulty" issue is a total non-problem. This is partly the issue you face above, yes the sensitive nature of some proteins makes their study in some scenarios difficult, however it doesn't make it impossible. The mountain of data of which you are clearly ignorant shows this.
Synthetic chemistry isn't simply mixing everything together in a pot and hoping something comes out right. Nor is research into abiogenesis. Polypeptide synthesis can be accomplished very carefully. Again we have another Nobel Laureate for you, Robert Bruce Merrifield (Chemistry, 1984). He developed solid phase peptide synthesis (incidentally one of his papers on this is the 5th most cited paper published by the Journal of the American Chemistry society, it's impossible to miss!). In the 1960s his group synthesised bradykinin, insulin, and ribonuclease A to name but a few. All proteins, all with biological function. Again, these proteins are just polypeptides.
So do you mean synthesis as in the careful construction of molecules or synthesis in the sense of "mix it together in a big bucket and out it pops"? If you are using the term in the latter sense to refer to abiogenesis then you're off your chump again I'm afraid. As I said earlier, no one claims that abiogenesis is anything like a big bucket of chemicals out of which some fantastically improbable and complex object pops as if by magic. This is your own strawman, a confection derived solely from your own personal ignorance.
Your witterings about co enzymes and co factors etc is just another manifestation of your abject lack of understanding and knowledge of the subjects at hand. Modern biochemistry is an evolved entity, not the starting point, yet again your issue is that you seem to think that there is some mythical highly complex organism/chemical entity that had to spring into existence in defiance of known science. Get this right out of your mind, that is not what abiogenesis is about or what it claims. Which brings me neatly to....
5) | Quote | Are you saying that micelles or autocatalytic reactions can be...ummm...randomly modified and then selected? All you are doing is pushing the buck back to something else that won't do the trick. Reminds me of physicists and their "dark matter" or Expansion Theory.
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I'm not saying it, it's a demonstrable fact. And no, no one is pushing any buck back to anything that won't do some fictional trick in your woefully ignorant understanding of what the relevant science is. The issue of copying fidelity is quite simple, if a replication process is 100% perfect then no copying errors can creep in, this means no diversity in the copies that are produced, they are all 100% perfect copies. However, if the replication process is not 100% perfect then the copies are not 100% replicas of their parent system. This means that there will be a diversity of imperfect copies, some will be better self replicators, some will be worse self replicators, some might lose the ability to self replicate at all. I suggest you go away and get a grip on the basic science of replication, and this won't be easy, it ranges from chemistry to computer science, and given your woeful misunderstandings of even the very basics of peptide chemistry I am not optimistic we will see anything useful from you on the subject within 5 years.
6) | Quote | | So, if your experiments are not conclusive, then it would be unethical to state that abiogenesis occured (see above). |
No one said that the experiments were not conclusive, yet another little straw man on your part. What I (and myriad others) said is that we know that abiogenesis is possible, that there are no physical barriers to it, that it could have taken many routes and we have yet to figure out which route it took. I'll give you an analogy to help you:
Here is some information: I live in London, I want to get to New York. At 9am on the 1st of January I am in London and on the 1st of March I am in New York.
We know there are many different ways to travel from London to New York. I could have flown or taken a cruise directly to New York, but I could have also gone across the channel to Paris and taken a flight from there etc etc. At some point, due to what we know about the geography of the planet, I must have crossed some water, either the Atlantic or Pacific oceans for example, to get to New York. At some point, due to what we know about the politics of various nations, I must have passed through passport control. We know I must have done this somewhere in the USA at least.
On the information I gave above we don't know what specific route I took but we know about some of the key stages I must have passed through to get there. There are unlikely scenarios like my rowing across the Atlantic single handed and creeping into the USA unannounced or my inventing teleportation to account for, but these can be easily ruled out by say a medical check up or a testing of my teleportation claims/devices etc.
Abiogenesis research is very much in this sort of position, in fact it's actually a lot better off than this anlogy allows but that's a digression. We know that it is very possible for me to travel from London to New York, we know some of the key stages it is very likely I passed through given the type of starting points and destinations I chose, and we know of several mechanisms I could have used to accomplish the journey. What we don't know is which I took. In the case of abiogenesis we know (for example) I stopped over in Paris, we also know a lot about journeys to Paris from London, however, we don't know a lot about journeys from Paris. Get the picture?
So no, RedDot, it is not unethical to teach about abiogenesis because, your massive ignorance of the topic aside, we actually know a hell of a lot about it.
You've got a lot of reading to do.
Louis
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Bye.
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