foodchain

So, essentially the electrons still travel in orbitals, just not orbits.

Its called the electronic configuration and I think it also ties into the periodic table. You have certain values if you will in which an electron can "occupy". This then leads to a probability of finding the electron I think in that certain orbital. This ties into the Pauli exclusion principle for shell filling or is that the Hund rule. So say you have iron, its electron configuration as cut and pasted from wiki is [Ar] 4s2 3d6. This tells you how many electrons and where they are at and a I think the closest living relative which in this case is argon.

I don’t know why its still called an orbital. Lots of QM goes back to Planck and really you have discrete values of energy. So a simple way to look at it is it takes so much energy to eject the first electron, and so fourth. I think this even has a name I just cant remember it. The thing about it is if you could say exactly where an electron was you would have to know both position and momentum at the same time. The electronic configuration and related variables are all products of QM I think. A good example of why QM works is because it could explain random decay and why the electrons did not simply crash into the nucleon.

If you go through the electronic configuration for an element it typically leaves you with the reactivity or amount of electrons and element has, or what shell is not filled for instance.

I think the question is ill-formed.

 

Energy "acting" in a vacuum sort of implies electromagnetic radiation, but that's certainly not the only way to transfer energy or the only form it takes.

I have to agree, I don’t know how to ask this question very well. Let me try to refine it.

I want to study potentials and kinetics of energy in small systems, say microbes, from individual to say a population. I want to study behavior as it relates down to a molecular level, looking at it from what form of energy may be doing what at a particular time, such as a chemical reaction or a constant string of such.

So for instance if you had a certain amount of use to a particular aspect of microbial physiology, what is the reaction of the microbe when an environmental effect changes say selective pressure, what happens to the thermodynamics of the microbe. Then the idea is relating this to reproduction, but I want to keep it all on a level of just recording the dynamics of energy in the microbe, regardless of form. My guess is that selective pressure or just destructive interference may play a huge role in homeostasis for instance, but the idea to me is trying to study such from a very reduced platform. Not in terms of even just chemical names, but just values of energy as it relates to potential and kinetic realties of microbial environment physiology/evolution.

I mean studies on microbial populations as they mutate for instance to overcome some barrier is neat, but in all reality why in regards to time can such an adaptation occur, giving all possible mutational routes the bacteria could take. Also when it finds one that is fit, energetically I would assume being the prime reason for such and the subsequent bloom of such genes in a giving population.

I just have no clue in the most basic sense of what physics I would even be looking to use. I can grasp what chemistry I would want to use, and of course biology, in a very general sense of course.

What do you mean oscillations in a vacuum?

 

Taking a guess I'd assume you meant vacuum fluctuations?

I guess that’s it?

What I am looking for is some basic introduction on potentials and kinetics of energy in a systems way. I thought a tendency of energy to act is via a vacuum? So I was wondering if oscillations became the form of that in some way?

What do oscillations in a vacuum resemble or do they exist? I was just wondering about that in application to say chemistry experiments. Could you apply such?

D'oh. Why didn't I think of that?

I dont understand it either, all you have to do to cheat that if its to guard something somehow is to highlight the text field with your mouse.

Would it be possible to basically make an energy production system for say civil use that runs for a certain period of time with a guaranteed performance utilizing a linear combinations of energy production. For instance the first step might be an extremely low powered one, and each step basically initiates the next until you reach a cyclic point from which constant energy for civil consumption is generated. I know it might make it sound like you need better and better efficiency but that should always be I think a priority anyway in design.

I was thinking aggregation of such a system could allow for easier maintenance, and of course changes to such technology. Its not only that but I think it would also segregate data into more easily digestible chunks for the advancement of such and of course controlling environmental effects. The interface to human aspect I think would also become more prominent if say every twenty or so years of use a new contract for use must be obtained which requires new industry standards to be emplaced again for performance and environmental impact.

I think space junk is going to become more and more a problem in time as such is already showing. This posses a serious threat to modern astronauts. I was actually quite amazed to learn that not to long ago really computer technology on a space shuttle was not so much about performance at all but really just dependability. I think it was green text only screens and stuff. With that being said this device would consist of a lot of material I would assume, so that alone to me again in the context of space junk is really an issue I think.

I don’t remember the number giving but a speck of paint in space can punch through a lot of material or something like that.

I like using the idea of integrated stuff, such as using say bacteria for a step in an otherwise electromechanical device for such sci fi stuff. Bacteria that can react to toxic waste or even nuclear waste might actually be able to provide some sort of realistic and safe remediation for existing problems and maybe even certain production levels. I know some species of bacteria have made homes in such environments, that alone is enough for me to think its possible.

I don't think "awesome" is the word I'd use to describe it, but it does seem like a reasonable idea to use nuclear power to create our liquid fuels. Quite realistic, even, if there weren't so many regulations on and people terrified of nuclear plants. By the time the bureaucrats and NIMBY's are satisfied, we will have found a better solution

 

In any case, the results should be applicable to fusion as well, if we ever figure that out.

I think France gets about 70% of its energy from national nuclear facilities right? So I guess its possible to integrate such technology into modern society but just like with fossil fuel consumption the environmental risk is nearly insane.

I don’t understand why energy has to have just one form for human consumption, and I would think that diversification would only lend to durability in times of uncertainty.

I thought that autotrophs were alive and well. What I was referring to as maybe having died out were pre-prokaryotes that did not utilize the complex interactions of DNA and RNA, but rather one nucleic acid that somehow does it all, seeing how the chances of two nucleic acids working in conjunction in a first working cell is a lot less likely to happen than one nucleic acid. Of course, that is pretty hard to fathom anyway. But even when you get into the area of protobionts, we are still looking at nucleic acids driving everything from inside, so really protobionts are what I was essentially referring to. I need to do more reading on it.

 

Also, I forgot all about the prions, proteinaceous "cells" that don't have DNA. It could have all started from something like this, but somewhere it had to form or acquire a nucleic acid, among other things, in this case.

Right, I can understand the DNA/RNA bit. I think you could easily just say it was simply a proteome like mass that did not react to natural selection until inheritance of some form became established, the reality though is using inheritance for the only definition of life via DNA/RNA is why such statements fall to the wayside. Everything is gene centric in view, its crappy I think if you happen to hold theoretical ideas. I guess it sounds like a logical goal really, but I just don’t understand giving evolution in the first place why to make the view so narrow, even just using carbon-hydrogen bonding its hardly like we know all the possibilities.

Yeah, I hear what you're saying. I've been trying to think up some other way, some thing that a prokaryote could have evolved out of, but no luck so far. Maybe I should read some of these MIT articles. The abstracts seem fairly straightforward and most of it seems built around the classical model, but maybe there are some alternative ideas nestled in there.

Well here is a weird question. Say you have a trophic system. The bottom of that is microbes. So is the microbe sort of like the plug in for a power socket which in turn powers genetics for instance? I know its a weird way of wording it but if autotrophs simply died out the rest of evolved life on earth would follow simply because of evolution. So thermodynamics would seem important but that all implies energy/matter stuff over time, not that in some instant the organic soup was just right out of the blue with no past.

Well, the way I look at it is that it all had to start somehow. I am using the assumption that it all started with a do-it-all type of nucleic acid, something that is no longer present because it is long obsolete. RNA/DNA works better. Maybe the first replicator died out when the earth became oxygenated. Maybe the type of prokaryote that this first replicator helped form died out for whatever reason soon after it mutated and formed the prokaryotes that we know of today. There's a lot of maybes, but it had to happen somehow and there has been a lot of research into how it may have happened, how we can maybe make it happen today in the lab. If we can make it happen in the lab, then given the vast scale of the raw undeveloped earth, why couldn't have it happened there? The logistics are the only limiting factor, but there had to be a way, period.

 

All Mr. Wickey is doing is demonstrating how the primary building blocks may have formed, and it had to have happened in a hot spring. Ocean vents would have had water that was much too diluted for it to occur there.

Primary building blocks of what? That is also an assumption. You cant say past life on earth what chemistry is required in what environment really, but that’s mildly beyond the point.

The environment as you point out with the vents is entire subject of its own, the abotic conditions. Whatever clocks geologic functions run on, which are usually forever to abrupt on up to the atmosphere are surely of massive impact. Your are then faced with the very real possibility at least in my opinion that geologic environments like the lithosphere or heck the asthenosphere or who knows may have been the breeding grounds to life on this planet. I agree fully with a historical approach giving the reality of organic evolution but I don’t know if I would look at it from any kind of a classical perspective really.

I think I would arrange it in terms of nucleotide density within the pond. Say you have 4 types of nucleotides and, for the sake of ease, equal amounts of nucleotides within the pond. One of the variables can then be "How dense is the nucleotide content within the pond?" This will then have an effect on how often additions to the chain occur and you can keep a running total of free-floating nucleotides within the pond, gradually decreasing as they get scooped up by valid ends of the sequences. It looks like it wouldn't be too hard to make it "chemistry legal", as certain nucleotides will only pair with certain others. Since we're only talking about 4 nucleotides, it shouldn't be that hard to enforce. Again, I am a bit out of my league here, but this is what I have read so far. It sounds a little more complicated, but I don't see how it would overwhelm the computer mathematically unless you start factoring in other processes such as tRNA, mRNA, DNA, and so forth. Even then, computers are pretty powerful and isn't it just a matter of time before it adds it up? Again, I really wouldn't know for sure.

I don’t know a whole lot also on the subject but really I don’t think its valid to just use dna. We have no idea what early life was or is or could be past microbes:D We can say protobionts but really what is that, a precursor to a possible prokaryote? What about RNA world and all that stuff.

Its like the thermodynamic argument. Who knows exactly what all can occur in a giving amount of energy. I mean a simple point is just to flick a coin with the same amount of energy on a surface, to trying to digest what all can occur on the earth in time within the constraints of that system whatever it may be concerning the fact the earth is not isolated in any sense. Its also I think hard to program in the reality of time. Billions of years is something I doubt any person can come close to realistically considering. More so within say "biological" time. The mutation some individuals carry in Europe that makes them immune to aids is a perfect example of that.

Lastly biology as studied by physical science is weird really. For instance electron density as related to photosynthesis is found to have easy properties to study by quantum mechanics, or papers exist on the topic. To me along with vision, the nervous system, chemistry and so on implies that such a theory can be applied to the theory of evolution. How hard do you think it will be to discovery all of what evolution and QM have in common alone?

I think the software sounds nice but its I think outside of something a typical computer could really calculate at least. Also I think it would be pretty evidence that science does not posses some mathematical quantization of evolution that certainly satisfies for what has occurred, but to me that does not say much. I mean you could plug in some population genetics stuff really on a giving selection of genotypes of genomes, but without a way to actually see just that part of life in action with the rest, like the proteome for instance I also doubt would really be useful for solving evolution. I also don’t understand how you are equating the environmental relationships really. I guess some form of a probability might be able to generate results, but I doubt that it would represent really evolution past just showing a Darwinian mechanism.

I am not thinking that you are trying to make some software that will automatically show various ways in which you might become a penguin, just that I don’t think you can really model evolution if you don’t have all the parameters in the first place. I mean tomorrow or next month some new discovery will come along that seriously hinders such computer based modeling if the modeling itself is not really scalable constantly. I was at a database site not to long ago on the web which listed just human biological processes and the current number of such was astounding to say the least.

The point of the thread is that microbes are the closest living ancestor we have to whatever primordial life was in regards to origin of life, which origin of life implies biological system. As far as particular microbes go prokaryotic life arose before eukaryotic life, this can be evidence on a molecular level I believe with studies using horizontal gene shift, of course that’s not the only way.

Also for what its worth the amount of life in the earths crust is to be a far larger amount of biomass then what is on the surface or oceans for instance. I would imagine that such also has its own unique biomes though I don’t know if you can apply such a word to it. I mean microbes are being found that are becoming increasingly different the common or known species. Plus the relationship between microbial life and flora is also very interesting to me.

Tardigrada for instance is very unique. Not only in bauplan but in ability to survive extremes of radiation, temp, and basically I think it can survive in the vacuum of space. The reality of cryptobiosis is very interesting to me more so in an evolutionary sense of why it has come about through natural selection. Basically I think going past microbes really in questions regarding origin of life is somewhat pointless really.

So, basically... you have set some arbitrary goal post for the spot where life began, and you're calling that the microbe. Okay. Whatever works for you.

Well I don’t know if it were truly first thing to qualify under the current definitions of life. I do think again that its the closest living ancestor of such. More so with the prokaryote or bacteria. I think its the most bare organism for study with physical science alone if you will, or if that’s not a good way of looking at it, I think it at least has less overhead compared to say a much larger multicellular organism.

Maybe its just human vanity perhaps that reduces the role of the microbe in the world, I don’t know really.

I don’t think so.

I think you could just as easily as say become a geologist, or a physicist. Origin of life does imply life, while a microbe would imply chemistry its hardly just a redox reaction or what not. That’s sort of like saying well if you want to study chemistry, you should become a biologist, I just don’t buy it. Plus giving evolution in which natural selection and such would at some point become intertwined with whatever other physical mechanism that lead to life in the first place. You have to be able to apply or look for the biological aspect even if its precursors looked nothing like it.

I mean what lead to life might have been certain inorganic clusters of materials at a certain depth or pressure or what not in the earths crust? So really to me using basic evolutionary thinking and going along on a history or timeline approach the microbe to me is the closest living relative to origin of life if not it in of course an evolved form like every other living thing, so to me the ecology of origin of life should satisfy using microbes.

What do you mean by "prime target" and "go past"?

 

The reason why humans are the 'target' in a lot of studies is because studying humans is directly relevant to things like medicine.

However, this is not meant to suggest that we think that evolution has 'stopped' with humans. We are constantly evolving and these changes are measurable.

 

 

Evolution of microbes is a strongly emerging field in the study of medicine, but there are still applications for studying evolution in different model organisms...

For example, studying a bacteria isn't going to tell us much about the common ancestor of chimps and humans.

You are right on about the medical application of microbes, but they hold so much other promise in many other areas also, such as bioremediation to bioengineering really. I think microbes also hold promise for the application of physical science to biology more so then other biological systems, plus you don’t have some of the more common ethical issues such as blasting some animal in a cage with a concentrated gas to see if it dies or gets cancer or what not.

I don’t want to get off on the wrong foot thought in regards to microbes. I am not saying just study them in regards to evolution, but I do think that they are the first line in trying to study origin of life questions using biological organisms, that is all.

What's the point of this thread?

 

 

Evolution is not quantized, however... I don't think even the punctuated equilibriumists would go that far.

Quanta are discrete units of energy of specific values. So in regards to the thread basically to go from origin to life to human being, or using the human being as your prime target I guess for trying to explain life or the origin of such I think only degrades such a process when in all reality I don’t think a person should really go past microbes.

So the point of the thread to me, I think is that using microbes is a better conceptual framework then trying to use just humans. I think it ignores evolution, and I think it misses really the reality of microbes.

So if the use of words confused you, sorry, it was just figurative speaking really.

I think a modern confusion over origin of life studies is perspective. I mean a small perspective. Microbes are not bony creatures, they do leave behind evidence but you have to remember the timeline you are looking for such combined with the fact similar behavior to what you are looking for very well may have eaten such evidence literally.

Microbial life, its so tiny that getting much farther away from it can give you the title of not even being alive in the case of the virus. Giving the concept of evolution, time and of course natural selection it might be safe to assume that primordial life may have been not much more the viral like clusters of matter, to much most anything. When thinking of origin of life microbial life is the closest link we have to such, beyond that trying to go from origin of life to say human I think is almost a quantum leap that leaves out the middle and lessens the reality of the beginning with the microbe when thinking about such a question.

 

 

Can anyone see anything else?

 

I would also greatly appreciate any positive comments for my efforts. Any one think this is a good idea? Anyone interested in the software? Please let me know. Post a warm thanks.

 

Thanks from me in advance.

 

Jerry

Creationists were not right about much anything I can think of. On your program which sounds very nice btw, do you account really for the proteome and how do you go about such?

yeah, it`s just a nice way of knowing how efficient something`s going to be in terms of reaction energy In and Energy out, without ever having to lift a test tube

 

the only problem I have is that there`s nothing listed for Metal bonds, so I can`t even say how much energy is given off if I put say 1g of Calcium metal in some water

 

I have a feeling that I might be missing something very simple OR I need a more comprehensive table.

So you could graph something like that pretty easy huh?

*Is this the kind of stuff you are talking about?

http://www.jbc.org/cgi/content/abstract/282/8/5853

it`s no actually hard to understand, so i`ll give it a shot and try and explain

 

take Methane for example (CH4) we know it burns in O2 (oxygen in the air).

 

if we look at a Methane molecule we`ll see if has a central Carbon atom and 4 hydrogen atoms around it each making a single bond.

so we have 4 C-H bonds.

each C-H bond requires Energy to break it, this number is Delta H +

the number is Positive because it Requires you put in Energy.

 

O2 in the air (is a double bond IIRC) like O=O, this also requires energy to break it

now to Burn Methane in O2 we make the equasion: CH4 + 2O2 = CO2 + 2H2O

so we add up the one side of the equassion in terms of Bonds to be broken

 

C-H bond (there`s 4 of them)

and O=O bonds (there`s 2 of them)

 

you look these up in a book (unless you remember all the Bond enthalpies) and you arrive at a number.

 

you then do the same to the Other side (your reaction products).

 

you then take one number away from the other.

 

the Difference is the Overall enthalpy of reaction and it will not only tell you if it`s an Exothermic reaction or not, but Also How much energy is given off

 

this is a Very basic explanation but illustrates the principal nicely I hope

So its an enthalpy equation?

A combination of Lamarckian and Darwinian evolutionary processes?

No.

Basically in my idea if you subtract natural selection from evolution I don’t think anything makes sense. So from DNA to concepts like environmental physiology how does natural selection actually apply pressure? Say any multicellular organism or unicellular. I think unicellular provides a basic insight for how multicellular lifeforms survive as a total organism and of course from studies on such which bring about physical data like sugar phosphate backbones and what not to make things short. So from the success of physical science in biology I wonder how much of natural selection can be defined on such a small level, such as cellular molecular for instance. For instance can natural selection tend to favor the probability of mutation in certain places or rate of mutation to certain genes?

I know the general idea is one of reproduction in time favoring traits in units or unit traits or what not from a fitness landscape, but with the concept of epigenetic networks for example and norm of reaction for another how well is natural selection wired into the smallest aspects of biology? Can disturbances in such lead to developmental issues? I would think so rather easily but in how many forms? Basically maybe you could trace selective pressure and map such. I think if that could be understood I think it would have huge applications, a person could learn exactly what behaviors to dodge to avoid triggering some gene or genes to become active or inactive possibly to concepts in biological engineering for another, I think it would also greatly enhance ability to understand environmental impact really.

no, I wouldn`t have said so, esp when you consider that the iron and carbon in steel are in fact individual crystals, more akin to an Alloy than anything else I reckon.

 

Carbides on the other hand??? that`s a toughy, I don`t really know enough about the exact definition of what constitutes a proper organo-metalic compound, so I can`t answer that one for you.

 

it`s strange in a way, because my Question a couple of posts up occurred to me when I was trying to work out the Delta H of calcium carbide in water (it`s very exothermic).

and then I realised I have no listing for any of the Metal bonds to complete my calculations DOH!

I don’t really know what you are talking about. In steel I don’t know if the bonding is qualifying either. As for your problem I don’t understand but it sounds interesting. Is it a reaction mechanism type thing or something about apparatus or environment if that stuff is separate from reaction mechanism. To be honest I don’t hold a total understanding for what reaction mechanism is to mean.

I have a quick question on this topic.

 

my Data book lists most all the bond enthalpies used in chem (Organic) so all the O-H and C-C and C=C type stuff is in there, and for the most part it`s pretty useful.

 

but there`s Nothing listed for Metals?

 

so How would I work out the Delta H Na+H2O ---> NaOH + H

 

Sodium isn`t listed in there.

 

do I need a better book, or is there a way to find this value?

Organometallic stuff, I think it involves carbon. Does that make steel a Organometallic compound?