Abiogenesis

[lunamoth]

Abiogenesis, not evolution, addresses the creation of life from non-living forms. I thought it might be interesting to explore this theory here, and also to ask a question.

The current model of aboiogenesis (I am not an expert, I'm taking my info from Talk Origins) simplified goes like this:

simple chemical-->polymers-->replicating polymers-->hypercycle-->protobiont-->bacteria

My understanding leads me to accept that given enough time and the right conditions this might be possible. Various parts of it have either been recreated in the laboratory or observed in nature, for example Self-reproducing system can behave as Maxwell's demon: theoretical illustration under prebiotic conditions. To me the obvious big jump is from a hypercyle (whatever that is) to a protobiont.

From the online article:
"..., because in modern abiogenesis theories the first "living things" would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria is given below."

I hope the explore this further online and share what I find here for your critiques, but for now one question has occurred to me that some of our members might be able to answer.

Is there any evidence for the existence of any of these protobionts or the step between self-replicating systems and a protobiont in nature today (outside of bacteria and cells--I know things like prions and RNA enzymes, not to mention all viruses might qualify, but they are only found inside cells)? If not, is it because we are no longer a "primordial soup" conducive to abiogenesis? What would cause abiogenesis to stop? Has it stopped?

Once organisms got to the point of performing chemical reactions (metabolism), they themselves could vastly alter the environment (i.e., the creation of toxic oxygen by photosynthesis, in turn paving the way for organisms utilizing respiration). But even chemosynthesis is way way way down the line from protobionts.

Any thoughts?

lunamoth

P.S. Talk origins addresses a lot of the objections put forth by creationists and ID proponents about the calculations for "life," if anyone is interested.

 

[path_of_one]

Interesting, though I'm afraid I don't have much to offer. The only thing close I could think of is a prion, and as you pointed out, they need cells to reproduce. The interesting thing about prions as compared to viruses though is their relative simplicity (no protein coat) and their durability. The discovery of prions definitely points to a category of sort-of-but-not-quite-living at least.

Of course, the whole subject of abiogenesis is, in some way, culturally framed. We distinguish between life and non-life, and between life with consciousness and life without. Some cultures see everything as life, or everything as life with consciousness. It reminds me of a Native Californian saying my advisor told me once when I told him trees were "people" too- "Rocks are people too. They're just quiet, slow-moving ones."

Who knows? Maybe really everything is alive, and we only perceive it to not be so.

 

[Tao_Equus]

Nice one Lunamoth!! This thread has long awaited its genesis !!
As this thread is so specific I am going to have to go back to my old textbooks and delve into new sources such as you suggested before making any contribution. I know the last time I had a look at the subject there seemed to have been very little hard research done in this area. Perhaps the recent rise of dogmatic creationists in the US has now forced the hand of evolutionary scientists.....I hope so.
At the outset though I would pin my colours to the mast that Path-of-one raised above.....that its how you define life/that everything is alive.
I look forward to the evolution of an interesting thread

 

[lunamoth]

Greetings Path-of-One! So great to see you around more regularly again!

Hello Tao Equus, I've been appreciating your posts in the evolution threads, as well.

I have not had any more time to research this any further--probably could get more info by refreshing on some intro bio books, but I have a feeling that I wouldn't get much deeper there than I already have outlined.

I put it here in Belief and Spirituality because I'd like to hear more from people who might take a more cosmological or philosophical view of these types of questions. I mean after all, it's a BIG universe.

No matter how high the odds against life forming on our particular world in our particular universe with the amazing aptness of the physical laws and conditions we observe and deduce, life has indeed emerged. Odds are always odds. And of course there is the observation that until those odds were beaten no consciousness would exist to contemplate these questions.

There may be gaps in our knowledge, there may always be, but I don't see any use in filling those gaps in with Goddidit. In my view, He did it all, what we understand and what we still don't understand, and left us the task of appreciating the very fine work of His creation.

What is that Sherlock Holmes line? Something like "no matter how improbable it is, when all else is ruled out what remains is indeed the solution."

peace,
lunamoth

 

[juantoo3]

Kindest Regards, all! Really nice to see you back, path of one!

Thanks for raising this, Luna! I am afraid it is a bit out of my league for the moment, but I am sure I will love where it goes.

I do have a curious thought though that lingers from the other thread. What is the role of E=MC2 in this? That is, is spirit a form of energy, and if so, how or does it tie into the equation considering life, particularly at the single cell level? Is it possible, that if spirit is endemic in matter as energy, that the process is not "if" but "when?"

Just a thought.

 

[lunamoth]

Kindest Regards, all! Really nice to see you back, path of one!

Thanks for raising this, Luna! I am afraid it is a bit out of my league for the moment, but I am sure I will love where it goes.

I do have a curious thought though that lingers from the other thread. What is the role of E=MC2 in this? That is, is spirit a form of energy, and if so, how or does it tie into the equation considering life, particularly at the single cell level? Is it possible, that if spirit is endemic in matter as energy, that the process is not "if" but "when?"

Just a thought.

Hi Juantoo3.

Wow, you raise a really good point and I am glad you did. I'm sure others will disagree with me, but I do not view spirit or as energy or anything at all governed by the laws of physics. I place it very much in the realm of Mystery. Doesn't metaphysical mean 'more than physical?'

peace,
luna

 

[juantoo3]

Kindest Regards, Luna!

Doesn't metaphysical mean 'more than physical?'

While I am inclined to agree with your definition, is not the term but a label, one used because we simply do not know?

I do not mean to imply that all energy is spirit, what would be left to become matter? I mean that spirit might be one kind or form of energy, out of how many kinds we are still discovering?

 

[lunamoth]

Kindest Regards, Luna!



While I am inclined to agree with your definition, is not the term but a label, one used because we simply do not know?

I do not mean to imply that all energy is spirit, what would be left to become matter? I mean that spirit might be one kind or form of energy, out of how many kinds we are still discovering?

OK Juantoo3, you are right about my circular logic there.

Well, I think that our soul spirit falls outside the realm of anything measurable except by the human heart, soul. Not energy, not "light" in the physcial sense, not physical at all. But hey! I might be wrong. When you get the data please share it with me.

cheers,
luna

 

[juantoo3]

If ever I find the data, I will be happy to share.

Which is why I asked in the form of a question...

 

[Tao_Equus]

Thank you for your warm welcome Luna.

I think some form of energy is the key here. Recently there was an extremely interesting TV program on here in the UK Regarding the findings of a few geneticists. One in particular, a doctor called Marcus Pembrey and a clinical geneticist at the Istitute of Child Health in London noticed that mutation in a particular gene would cause different diseases in different people. Something that confounds genetic theory. Further research revealed that the gene somehow remembers whether it was inherited from the mother or the father and causes a diffrent disease with respect to its source.
Why is this relevant here? Well up until now we have considered DNA to be the definitive blueprint of life. That it's arrangment of genes is the be all and end all of what information is being passed on. But this is clearly not the case. I suspect, an unsubstantiated leap of faith I admit, that it is some form of energy that carries this additional information. And further I suspect that its a case of some kind of quantum entanglement.
If you begin to imagine quantum entanglement not in terms of a single pair of intereacting sub-particals but as a vast sea, a matrix, of countless zillions of communicating points, unconstrained by the limitations of relativity what do you have? You have an all seeing, all knowing omnipresent energy.
However this is not getting down to the nitty gritty of what is provable in terms of abiogenesis. I will be back


Regards

TE

PS. Here is a link for anyone interested in the program mentioned above; http://www.bbc.co.uk/sn/tvradio/programmes/horizon/ghostgenes.shtml

 

[Bandit]

Abiogenesis, not evolution, addresses the creation of life from non-living forms. I thought it might be interesting to explore this theory here, and also to ask a question.

The current model of aboiogenesis (I am not an expert, I'm taking my info from Talk Origins) simplified goes like this:


Any thoughts?

lunamoth

P.S. Talk origins addresses a lot of the objections put forth by creationists and ID proponents about the calculations for "life," if anyone is interested.

in the beginning...simple chocochemicalolis made the impypolymersals which formed the replicating solitpolymersuvica which made the hypercycle into protobiontockybookyocky that made ickyolabacterialisation...the end

 

[juantoo3]

Kindest Regards, Tao Equus!

a doctor called Marcus Pembrey and a clinical geneticist at the Istitute of Child Health in London noticed that mutation in a particular gene would cause different diseases in different people. Something that confounds genetic theory. Further research revealed that the gene somehow remembers whether it was inherited from the mother or the father and causes a diffrent disease with respect to its source.
Why is this relevant here? Well up until now we have considered DNA to be the definitive blueprint of life. That it's arrangment of genes is the be all and end all of what information is being passed on. But this is clearly not the case.

I read the reference you mentioned and I find the info interesting, but not at all surprising. I had the great fortune of finding the transcript of the interview with Drs. Francis Collins and Craig Ventor. If I may be allowed to present what I feel are relevent clips of the conversation:

DR. ERIC LANDER: There are far fewer genes than we expected, only about 30,000 or so rather than the figure of 100,000 in the textbooks. There is a lesson in humility in this. We only have twice as many genes as a fruit fly or a lowly nematode worm. What a comedown.

CRAIG VENTER: It makes it different than a lot of people expected. I think we were being fed this notion that you get one gene, one protein, one drug. (*emphasis mine) Out of the biotech industry. The number of those that's going to be happen is going to be counted on both hands probably. What's going to happen is we have to go into the protein world to really understand where the genome is taking the next level of biology. That's ten times as complex at least. … But I think the challenge is understanding the complex of all these pieces working together so that you and I can have this conversation.

DR. FRANCIS COLLINS: Well, I think the book is different than we thought. It tells us because we have only about a third the number of genes that we expected that those genes must be particularly clever in carrying out their functions. (*emphasis mine) We're still just as complicated as before we figured this out, right? So it must mean that our genes have a certain elegant way of doing multiple tasks more so than perhaps than simpler organisms do. For me as a physician, as somebody who is really interested in tracking down the genes that contribute to disease, to heart disease, to colon cancer, to diabetes, to Alzheimer's Disease, it means that the number of genes we have to deal with and sift through is a shorter list. And that's good news. That means we should be able to find the ones we're most interested in, somewhat more easily. Our haystack isn't quite as big as we feared it would be. That should advance the rate of progress in the medical consequences of this project, which is really the reason to do it.

CRAIG VENTER: So instead of the simplicity view of life which we had a large number of genes and there was a gene for everything, in fact, the fact that we have fewer genes means we have to understand these next levels of complexity much more than we would have otherwise.

DR. FRANCIS COLLINS: There's actually data now to support that. We've done a systematic comparison as have the scientists at Celera of the proteins that we humans can make. How do they compare to worms and flies? The numbers of genes are not that different but the number of proteins can be significantly different, and you can get more out of a gene if you're a human. (*emphasis mine) If you look at proteins, they're interesting. They have acquired additional domains, additional properties along the evolutionary process. Think of it this way: A worm protein needs to cut another protein called a protease, it will do -- it will do it really well but may not do a lot of other things. The human counterpart may not only cut the protein but be regulated in some way. If they've got the cutting knife, we've got the Cuisinart that you can set all sort of slicing and dicing options to instead of just doing one thing. So our come complexity is recovered, our self-pride is recovered. We're really just at complicated. It comes about in a different way. The simple idea that gene count explains everything has gone out the window. (*emphasis mine)

CRAIG VENTER: This is our first look now. It's so much information it's taken both teams the last seven months since gathering the data and getting it put together to really try and see what it means. Only a little over 1 percent of those 3 billion letters code for proteins. (*emphasis mine) If you'd asked any of us a year ago, I would have said 3 percent. A lot of scientists would have said 5 to 10 percent. I think we're all stunned that it's in the 1 to 2 percent range. … They're all A, C, Gs, and Ts to find out the right pattern to interpret and say this looks like a gene. But one of the questions you might ask is what is different in our genome from a fruit fly? We have roughly twice as many genes. Do we just have two of everything or are they more complex like Francis said? In fact, they're definitely more complicated (*emphasis mine) but we see specific sets of genes that expanded in the last 600 million years. We have an immune system; we have a blood system -- a great expansion of the central nervous system but the most interesting category that fits with all the things we've been talking about is we see a huge expansion in the genes that are responsible for regulating the expression of other genes -- so more complex networks and interactions with the same basic components. (*emphasis mine)

CRAIG VENTER: … studies at NIH a few years ago showed that in fact the X chromosome the gene order on the human X chromosome is identical as far as scientists could tell at the time to the gene order on the cat X chromosome. I think we only found one or two differences from the mouse X chromosome. Yes, we have the same parts and really puts the emphasis on this difference in regulation, the timing, the rheostats that says these genes should be turned on now. (*emphasis mine) Some people have argued the entire difference between us and chimpanzees is just in the regulation of the gene expression.

DR. FRANCIS COLLINS: And we shouldn't overstate that there's a small number of genes between us and other species because if you look at the genes we share they probably do have subtle differences. If there are only a few hundred genes that differ between us and the mouse, it doesn't mean that you could put those genes back into the mouse and the mouse would start singing opera and playing golf. There would be all sorts of other differences in all of those other 30,000 genes that are subtle enough to have a pretty significant effect. (*emphasis mine)

http://www.pbs.org/newshour/bb/health/jan-june01/genome_2-12.html

Please note, only 30,000 genes out of 3 billion base pairs on the genome, as well the acknowledged fact among *knowledgeable* researchers that human genes "multi-task." So I can see how this can easily translate into intergenerational and residual affects on the genome sequence. I hope my emphasis also noted how we share so much of our genome with other creatures; not just simians, not just mammals, but even fruit flies and nematodes, and as noted elsewhere in the interview, even with yeast. Which leads me even further to believe all life is inter-related and inter-connected.

My two cents.

 

[lunamoth]

in the beginning...simple chocochemicalolis made the impypolymersals which formed the replicating solitpolymersuvica which made the hypercycle into protobiontockybookyocky that made ickyolabacterialisation...the end

Eureka! I do believe he's got it!

Welcome aboard, Bandit.

lunamoth

 

[juantoo3]

BTW, the "knowledgeable" comment made above is not directed at you, Tao Equus. Just so there is no confusion.

 

[lunamoth]

Please note, only 30,000 genes out of 3 billion base pairs on the genome, as well the acknowledged fact among *knowledgeable* researchers that human genes "multi-task." So I can see how this can easily translate into intergenerational and residual affects on the genome sequence. I hope my emphasis also noted how we share so much of our genome with other creatures; not just simians, not just mammals, but even fruit flies and nematodes, and as noted elsewhere in the interview, even with yeast. Which leads me even further to believe all life is inter-related and inter-connected.

My two cents.

Hi Juan, Thank you for sharing that interview. I also found it very interesting. Note that the two key areas of investigation now will be protein expression and regulation of that expression. Perhaps it's like the difference between building a kids club house and a mansion. Same building princples, same or similar building materials, probably mostly the same tools. I also find a deeper meaning in seeing how much we have in common with other organisms, all being interconnected in this very fundamental way.

Cheers,
lunamoth

 

[lunamoth]

Thank you for your warm welcome Luna.

I think some form of energy is the key here. Recently there was an extremely interesting TV program on here in the UK Regarding the findings of a few geneticists. One in particular, a doctor called Marcus Pembrey and a clinical geneticist at the Istitute of Child Health in London noticed that mutation in a particular gene would cause different diseases in different people. Something that confounds genetic theory. Further research revealed that the gene somehow remembers whether it was inherited from the mother or the father and causes a diffrent disease with respect to its source.
Why is this relevant here? Well up until now we have considered DNA to be the definitive blueprint of life. That it's arrangment of genes is the be all and end all of what information is being passed on. But this is clearly not the case. I suspect, an unsubstantiated leap of faith I admit, that it is some form of energy that carries this additional information. And further I suspect that its a case of some kind of quantum entanglement.
If you begin to imagine quantum entanglement not in terms of a single pair of intereacting sub-particals but as a vast sea, a matrix, of countless zillions of communicating points, unconstrained by the limitations of relativity what do you have? You have an all seeing, all knowing omnipresent energy.
However this is not getting down to the nitty gritty of what is provable in terms of abiogenesis. I will be back


Regards

TE

PS. Here is a link for anyone interested in the program mentioned above; http://www.bbc.co.uk/sn/tvradio/programmes/horizon/ghostgenes.shtml

Hello Tao E, I have to admit I did not listen to the program you linked to. I guess I am being lazy. From your description I can't really tell how what you describe confounds genetic theory. In gene expression, like most things, context matters quite a bit. For example, is the trait sex-linked (dependent upon an X or Y chromosome?). Probably not since that should be quite obvious, but anyway, seems a bit premature to start invoking an as-yet undetected new energy, or spirit.

Yes, I am quite a skeptic.

For the record, at my current level of information I see many large and unfilled holes in the abiogenesis model, much more so than for the ToE.

lunamoth

 

[juantoo3]

Thanks Luna!

I think this interview also highlights another very important point, that a single particular gene is not very likely to be the source of "behavior," that is, and in accord with another interview of Dr. Collins I heard (and even quoted in a medical ethics class paper), it is not very likely that there exists some particular gene for drunkenness, or homosexuality, or thievery, for examples. I really do think there is way too much emphasis put on the genome in an attempt to explain away our ills or rationalize our behaviors. To be sure, there are medical conditions that can be explained by our genome. But not everything is genomic. Some things are just the choices we make.

Another two cents, and I hope not out of line.

 

[lunamoth]

Thanks Luna!

I think this interview also highlights another very important point, that a single particular gene is not very likely to be the source of "behavior," that is, and in accord with another interview of Dr. Collins I heard (and even quoted in a medical ethics class paper), it is not very likely that there exists some particular gene for drunkenness, or homosexuality, or thievery, for examples. I really do think there is way too much emphasis put on the genome in an attempt to explain away our ills or rationalize our behaviors. To be sure, there are medical conditions that can be explained by our genome. But not everything is genomic. Some things are just the choices we make.

Another two cents, and I hope not out of line.

Not out of line at all, Juantoo, and I quite agree. I think it would be astounding to find something like a single gene for behaviours as complex as tendency to addiction or homosexuality.

'Course, we are getting quite ahead of ourselves here, since we are talking about how does a replicating molecule find itself in a lipid bilayer bubble with no transport proteins without using up whatever substrates inside it needs for synthesis and then also grow its bubble for splitting off when it gets too big.

I'm kind of free-thinking here, don't take it as science, I'm sure others have done a much better job at it and had their ideas published by now.

But it does bother me how, if that lipid bubble is doing anything useful for the replicating system, that it is also not so complex that it also needs some type of synthesis and regulation, which is starting to get pretty sophisticated metabolically. Seems like a kind of a chicken and egg situation.

Anyone out there following me?

lunamoth

 

[lunamoth]

Actually, another thought about all this, and it is related to the observation that we see so incredibly much junk DNA in the genome, is that DNA is "selfish." In that, the bigger the molecule, the more chances that something in it is going to be useful. Could apply to RNA as well, if we postulate an "RNA World" for abiogenesis.

Another astounding thing to me is the leap from replicating nucleic acids to systems that assemble proteins based upon the RNA pattern. Once we get to that point, it is easier for me to visualize evolution from these little protocells all the way up to plants and animals.

I guess I'd better read some Dawkins, if I can stomache his atheism, to fill in some of these gaps in my understanding. Anyone else have some suggested reading? (Besides Genesis, Bandit )

lunamoth

 

[lunamoth]

Hmmm, maybe it's just the cold medicine I'm on, but it occurs to me that ID proposes not so much a God of the Gaps as is does a God of the Odds.

lunamoth