Can we create life from scratch?

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Injecting desired genetic code into bacteria marks a significant advancement, yet it does not equate to creating life from scratch. Theoretical discussions suggest that assembling the necessary chemicals to create a living cell is possible, but current scientific understanding of cell complexity limits practical attempts. The first fully artificial cell is unlikely to exhibit intelligence or self-awareness, as it would function similarly to existing unicellular organisms. While nature has historically relied on existing cells to create new life, the potential for synthesizing life from non-living components remains an intriguing area of exploration. Overall, the conversation highlights the complexities and uncertainties surrounding the origin of life and the conditions necessary for it to emerge.
  • #31
Well, thank you all.
I got my answers, actually, a lot more than that.
But the discussion is getting more interesting, let's see how far the radius gets stretched.
 
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  • #33
I wish to make two points:
First, I don't believe the chemical pathways that Jack Szostak described are as close to resolving the "Origin of Life Mystery" as his video implies.

The physicist, cosmologist and astrobiologist, Paul Davies reported in his paper titled, "Does Quantum Mechanics Play a Non-Trivial Role In Life?" that "imple calculation shows that it would take much longer than the age of the universe, even if all the matter in the universe consisted of pre-biotic soup, for even a single protein to form by chance..." and that "...the classical chance hypothesis [to explain the Origin of Life] seems unsatisfactory."

Is Dr. Davies correct in his opinion?
Richard Cevantis Carrier (who is an historian and fervent advocate of metaphysical naturalism), reported on 46 "probability of life" studies in a 2004 paper in which Dr. Carrier argued that all of the studies which had rendered the natural origin of life to be statistically impossible (one change in 10 to the 50th power or less) were flawed. Nonetheless, considering that the age of our universe is estimated to be 13.7 billion years (e.g. 13.7 x 10 to the 9 power years) the probabilities that Dr. Carrier reported seem incredibly small:
Barrow and Tipler (1986: 565) one chance in 4.3 x 10 to the 109 power
Borel, cited in Baudin (1962: 28) one chance in 10 to the 50 power
Bradley and Thaxton (1994: 190) one chance in 4.9 x 10 to the 191 power
Bradley and Thaxton (1994: 322–323) one chance in 10 to the 65 power
Bradley and Thaxton (1984: 145) one chance in 10 to the 117 power
Bradley and Thaxton (1984: 146) one chance in 10 to the 45 power
Bradley and Thaxton (1984: 157) one chance in 10 to the 175 power
Cairns-Smith (1984: 47–48) one chance in 10 to the 109 power
Coppedge (1973: 76) one chance in 10 to the 8,318 power
Coppedge (102) one chance in 10 to the 106 power
Coppedge (109) one chance in 10 to the 161 power
Coppedge (111) one chance in 10 to the 119,701 power
Coppedge (113) one chance in 10 to the 35 power
Coppedge (249) one chance in 10 to the 236 power
Coppedge (235) one chance in 10 to the 339,999,866 power
Cramer (1998) one chance in 10 to the 119,701 power
Eden (1967: 7) one chance in 10 to the 325 power
Foster (1993: 79) one chance in 10 to the 650 power
Foster (82, 172) one chance in 10 to the 88,000 power
Foster (39–40) one chance in 10 to the 68 power
Foster (52) one chance in 10 to the 163 power
Guye, via Lecompte du Noüy (33–34) one chance in 10 to the 243 power
Hoyle and Wickramasinghe (1981: 24) one chance in 10 to the 40,000 power
Hoyle (1981: 526–527) one chance in 4 x 10 to the 69 power
Huxley (1953: 45–46) one chance in 10,000 x 10 to the 1,000,000 power
Ludwig (1993: 274) one chance in 10 to the 2,300,000 power
McFadden (2000: 98) one chance in 10 to the 60 power
McFadden (98) one chance in 10 to the 41 power
Morowitz (1979: 99) one chance in 10 to the 399,999,896 power
Morris (1974: 60–61) one chance in 10 to the 53 power
Morris (64–65) one chance in 10 to the 450 power
Morris (69) one chance in 10 to the 299,843 power
Overman (1997: 54–55) one chance in 10 to the 536 power
Quastler (4) one chance in 10 to the 301 power
Quastler (6) one chance in 10 to the 255 power
Quastler (46) one chance in 10 to the 20 power
Quarter (58) one chance in 10 to the 6 power to one chance in 10 to the 30 power
Sagan (1973: 45–46) one chance in 10 to the 2,000,000,000 power
Sagan (45–46) one chance in 10 to the 130 power
Salisbury (1969) one chance in 10 to the 415 power
Salisbury (1971) one chance in 10 to the 600 power
Schroeder (1997: 91–92) one chance in 10 to the 850 power
Yockey (1992: 154–157) one chance in 2 x 10 to the 53 power
Yockey (1981) one chance in 10 to the 60 power
Yockey (1992: 154–157) one chance in 2.3 x 10 to the 75 power
Yockey (1981) one chance in 10 to the 125 power
(SOURCE: R.C. CARRIER, "The argument from biogenesis: Probabilities against a natural origin of life", Biology and Philosophy 19: 739–764, 2004.)

It should be noted that only six out of these 46 studies could support any argument that the natural origin of life was even possible within the time our universe has existed (13.7 x 10 to the 9 power years) with the most optimistic (Quarter, 58) providing a range of probabilities from one chance out of 10 to the 6th power to one chance out of 10 to the 30th power. It would appear that, at best, the probability that life arose naturally in accordance with the conventional scientific explanations is vanishingly small.

Is there an alternative?

I believe that there is, but will require a bounded quantum mechanical model to be introduced.
 
  • #34
What is the reference point for those studies? The probability that life evolves in a finite part of the universe, given our current laws of physics?

- if the universe is not finite, similar everywhere, and evolution of life is possible (we know that part), it will happen somewhere with probability 1.
- if MWI is "true", and evolution of life is possible (we know that part), it will happen.

The "probability" of fundamental constants? Every number is just pure speculation.
 
  • #35
Jacob Bronowski is arguably the coolest scientist to ever walk the planet. He had a good idea that DNA may have been initially formed in Ice. Makes more sense than an underwater thermal vent like we always see.
 
  • #36
Don't you agree?

https://www.youtube.com/watch?v=S8ecCnn5o1o
 
  • #37
The Stanley Miller and Harold Urey experimental creation of amino acids and Leslie Orgel's formation of adenine are necessary constituents of life but do not address the near statistical impossibility that many scientists have calculated for the "Origin of Life" in our universe.
 
  • #38
Their calculations are not worth more than the assumptions made.

But if the aim was to prove the life can't start, doing the calculations is a waste of time.
 
  • #39
Jon_Trevathan said:
The Stanley Miller and Harold Urey experimental creation of amino acids and Leslie Orgel's formation of adenine are necessary constituents of life but do not address the near statistical impossibility that many scientists have calculated for the "Origin of Life" in our universe.

Unfortunatley, as a biologist I have to agree with this. Our presence here is a near statistical impossibility in my opinion. And all those people talking about exoplanets are just pandering to the media. Still, I wouldn't be surprised if we found life on Mars, so I don't think anybody knows
 
  • #40
Paul Davies, in a 2004 paper titled "Does Quantum Mechanics Play a Non-Trivial Role In Life?", has suggested that "Quantum mechanics may offer a radical alternative ...[to the classical chance hypothesis]. Since quantum systems can exist in superpositions of states, searches of sequence space or configuration space may proceed much faster. In effect, a quantum system may 'feel out' a vast array of alternatives simultaneously. In some cases, this speed-up factor is exponential (Farhi and Gutmann, 1998). So the question is: Can quantum mechanics fast-track matter to life by 'discovering' biologically potent molecular configurations much faster than one might expect using classical estimates?"
 
  • #41
Jon_Trevathan said:
. In effect, a quantum system may 'feel out' a vast array of alternatives simultaneously. In some cases, this speed-up factor is exponential (Farhi and Gutmann, 1998). So the question is: Can quantum mechanics fast-track matter to life by 'discovering' biologically potent molecular configurations much faster than one might expect using classical estimates?"

I'm not sure I follow this argument unless it's based on the Many Worlds Interpretation of QM (MWI). Somewhat simplistically, MWI says that all states of a superposition occur, but only one state can be observed to occur in a given experiment. Other states are observed to occur in other "worlds". As strange as it sounds, it's favored by some physicists among those who feel QM needs an interpretation other than the "shut up and calculate" (~instrumentalist) one . How would you apply it here? Do we live in the "world" (represented by a particular outcome of a Markov process) where life as we know it did develop in the time frame we believe applies?

There's no clear argument that this is impossible or even unlikely without resorting to MWI or a role for QM other than its role in ordinary chemistry.
 
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  • #42
DiracPool said:
Unfortunatley, as a biologist I have to agree with this. Our presence here is a near statistical impossibility in my opinion.
Our presence here is, in fact, a statistical certainty: we are here. Otherwise, who are you talking to?

I wouldn't be surprised if we found life on Mars, so I don't think anybody knows
So... our presence is a near impossibility, but life on Mars is unsurprising?

I don't think many biologists still think that classical chance produced life - the "single protein from chance" type calculation are like the "hurricane creates aircraft" argument we get from creationists - with the same counter-arguments.

I think this thread is in the process of self-destructing.
 
  • #43
Thread closed temporarily for Moderation...

EDIT -- Thread re-opened. Thread is being monitored by the Mentors.
 
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  • #44
DiracPool said:
Jacob Bronowski is arguably the coolest scientist to ever walk the planet. He had a good idea that DNA may have been initially formed in Ice. Makes more sense than an underwater thermal vent like we always see.

You do seem to be taking both sides of the issue of the probability of life in the universe. Notwithstanding the obvious fact that carbon based life exists on earth, the question is: Just how rare/common is it in the universe? There simply is not enough data yet to answer that question with any confidence. However it's a fact that important compounds have been discovered in deep space and in meteorites (amino acids, cyclic aromatics, purines, pyrimidines, etc). These compounds are concentrated in water ice under extraterrestrial conditions and were likely delivered to Earth during the bombardment periods. I doubt the the surface of the early Earth was conducive to much ice formation. This should not be confused with the origin of life itself.

Given the availability of the chemical constituents of life and what we know about carbon chemistry, I don't understand this idea that life is such a low probability occurrence.

http://www.astrochem.org/sci/Nucleobases.php
 
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  • #45
SW VandeCarr said:
Given the availability of the chemical constituents of life and what we know about carbon chemistry, I don't understand this idea that life is such a low probability occurrence.

The problem is the (i) "Goldilocks" conditions required for a self-replicating peptide to form, (ii) inherent complexity of all known self-replicating peptides, and (iii) the requirement that the peptide be protected from all degenerative environmental factors until replication, and some evolutionary advances, have had time to occur.

As I noted above, Richard Cevantis Carrier argued, strongly, that all of the studies which I cited above and had rendered the natural origin of life to be statistically impossible (one change in 1050 or less) were flawed. He went on in his paper (on pages 749-750) to argue as follows:

"The appropriate mathematical methods and tools are formally discussed by Küppers (1990) and Kauffman (1993). In general, there are a minimum of five steps necessary.
First, we must identify the smallest possible self replicating protein and identify how many amino acids long it would be (which no one knows, though many guesses have been made).
Second, we must calculate the number of possible ways this many amino acids can be arranged into a string of such a length. Basically, the total t = ns [n to the s power], where n is the number of types of amino acids occurring in nature and s is the protobiont’s minimum length in amino acids. This requires including all the known varieties of amino acids (which is many times greater than the number assumed by all the authors who attempt this …).
Third, we must identify the “viability space” (v), the number of combinations within t that are self-replicating proteins (which no one knows, and no one but Coppedge and Eden have even tried to guess), since the odds of any entity forming by chance c in a single experiment will be v÷t. Almost all the authors who have attempted this have simply assumed v = 1, which is not even plausible, much less proven.
Fourth, we must repeat these three steps for all other protein chains of greater length (which no one has ever even attempted), up to the largest chain that can occur in nature, since we need the sum of all these probabilities, not just one of them. With this (and certain assumptions, see below), we can derive C, the odds of life forming by chance in a single experiment:
C = (vs + vs+1 + vs+2 + ... + vs(max) ) ÷ (ts + ts+1 + ts+2 + ... + ts(max))
Once we have calculated all the viable combinations for all possible natural chains, and divided that by all the combinations possible, we will have the odds that life will naturally arise in a single trial. The final step is to modify that result according to the number of possible trials that have taken place in the available space and time. The more trials, the better the odds. This does not mean on Earth alone, but throughout the whole universe. For instance, McFadden (2000) repeatedly complains about there not being enough materials on Earth to generate one random success, but the early Earth was just one pond among possibly trillions in the cosmos, and only one of those ponds needed to hit upon a successful combination."

In support of his argument that the statistics I quoted above are wrong, Carrier (on page 757) noted the following:
"We have created self-replicating peptides as small as 32 amino-acids long (Lee 1996), demonstrating that the smallest possible chemical that could spark life may be much, much tinier than anything any AFB proponent has assumed possible. McFadden calculates the odds against the Lee peptide arising by chance as 1 in 1041 (1996: 98), which is so far within the realm of cosmic possibility that it is already certain to have happened many times."

However, this statistic assumes the proper allocation and concentration of constituent chemicals and a means to protect the peptide from all degenerative environmental factors until replication, and some evolutionary advances, have occurred. Carrier responded to one of these criticisms as follows:
"And though some argue that cellular structure must also arise coincidentally at the same time, we know life in the right conditions can survive without a cell wall long enough to evolve one (organisms like viruses can survive outside cell walls), and cell-like chambers occur naturally in space (Cowen 2001), and under natural conditions on Earth (e.g. Goho 2003b; Morgan 2003; Horgan 1991: 119, 122), in which living organisms could take shelter, and over which they would gradually evolve a more complex control."
Nonetheless, and unfortunately I cannot find the citation, it is my understanding that these factors would again reduce the probability below 1 in 1050, which would again render the spontaneous generation of life in our universe a statistical impossibility.

This runs counter to my belief that life is common throughout the universe and has been the catalyst for me to look for a possible quantum mechanical solution to the problem.
 
  • #46
SW VandeCarr said:
You do seem to be taking both sides of the issue of the probability of life in the universe.

It's hard not to take both sides. The more I studied molecular biology in college the more astounded I was at the complexity of it all. DNA repair, translation, transcription, second messenger systems, metabolic cycles, etc. It all turned out to be much more involved than I had naively anticipated. I mean specifically metabolic processes that take many steps and have to be performed in specific sequences. It just seemed highly improbable that all this would have happened through chance. But yet it is all around us. So there's your dilemma and why I think its hard not to take both sides of the issue. It's just that it's difficult to wrap ones head around it intuitively.

I think that it will only begin to make more sense if and when we develop a sound model of how life originated, or find life elsewhere in the cosmos. I think we really need to know more about what life actually is and how it begins before we can make a reasonable guess as to how often it may happen elsewhere.

That's why I find origin of life research and discussions interesting. Bronowski's video is admittedly dated, but there's a good deal of current research going on in this area.
 
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  • #47
Theoretically, yes.

But first we need to understand a lot more about the structure and mechanisms of a living cell. We will also need a much higher level of technology. So It's possible. I don't think, however, that we have enough time to attain such a goal. We'll be long extinct.
 
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  • #48
DNA/RNA/proteins? They're puny wimps compared to the amount of information potentially encoded in post translational modifications. The only reason they get so much attention is because humans are good at figuring out codes and manipulating it, sorry life is not so simple. PTMs such as glycosylation are not template driven and can not be predicted so easily like DNA.

Sure, you can produce a protein by manipulating DNA, and have it even fold correctly, however many proteins don't work if they aren't glycosylated correctly. A PTM like glycosylation can control or influence everything from protein function, protein trafficking, cell surface organization, cell-cell interaction, and cell-matrix adhesion.

Carbohydrates and glycans are different than other biomolecules, not only is their sequence important, but so is their 3-D arrangement. Just how much information could potentially be encoded with carbohydrates?

Take for example 3 peptides. They can only be added linearly together, meaning there is only 6 possible combination. If you take 3 sugars commonly used in living organisms, the amount of combinations possible is 25,000. If you just expand that out to 6 sugars, the amount of possible combinations increases exponentially to 1,000,000,000,000 because of the ability of carbohydrates to branch in space. The amount of information that could be encoded in the 'glycome' and the complexity of it makes DNA look like the boy scouts and none of it is template driven. And not only do have the complexity of the glycome to deal with, different biology is achieved by further modifying glycans with other things like sulfation and phosphorylation. The complexity is mind blowing.


Carbohydrates were found in space for a reason...
 
  • #49
The complexity is mind blowing.

That reminds me, I do want to make one important embellishment to one of my earlier posts. I think the seminal (pun intended) problem here is to find out not just how life began per se but just how much of life there needed to be to begin. That's an issue that isn't often brought up if you're catching my drift. There's a bifurcation point between the formation of nucleic acid base pairs, amino acids, etc., and the point where the progressive-generative processes of evolution take over. I think these are the two mysteries we need to focus on. If you haven't read the book "The Sciences of the Artificial" by Herbert Simon, I highly recommend it. He makes a good argument for the almost inevitability of more complex forms arising from simpler ones once evolution takes hold. (But unless you reach that bifurcation point, complex forms tend to devolve due to entropy considerations). The parenthetical expression is my own musing, I don't know if this was in Simon's writings cause I haven't read the book in a while, but it's my personal opinion.
 
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  • #50
I think the ... problem here is to find out ... just how much of life there needed to be to begin. That's an issue that isn't often brought up if you're catching my drift.
You need to get away from the books more: it's brought up all the time - and it is not something that actually concerns empirical science ... it does not matter how much life was needed to kick it off. Empirically, you can only hope to find out how much there actually was. The rest is just math and philosophy.

Consider: It may be that there was more than the minimum "needed". Where would that leave you?
Though - ifaict, the "best models" currently are figuring a minimum life needed to be zero... it's a model that produces a lot of good science, and avoids misunderstanding, and that is pretty much what we need it to do.
 
  • #51
I think prions are a great clue how nature may have managed the feat of abiogenesis.
 
  • #52
Chronos said:
I think prions are a great clue how nature may have managed the feat of abiogenesis.

I remember writing a report on Creutzfeldt–Jakob disease for an epidemiology class I took way back when. I remember thinking how bizarre the whole model was. They didn't know much back then. I really haven't followed it since, but I think it's an interesting approach from what I remember of prions.
 
  • #53
@gravenewworld: Can you break a cell with a single modification of a PTM molecule somewhere?
The pure number of possible arrangements is not relevant, as long as different arrangements do not lead to different results.
 
  • #54
mfb said:
@gravenewworld: Can you break a cell with a single modification of a PTM molecule somewhere?
Sure, welcome to the world of O-GlcNAc modification:

http://cardiovascres.oxfordjournals.org/content/73/2/288.full
http://www.ncbi.nlm.nih.gov/books/NBK20725/

The pure number of possible arrangements is not relevant, as long as different arrangements do not lead to different results

Ah but different arrangements do lead to different results. How about a simple example? Sialic acids are carbohydrates that often cap the ends of glycan structures. Alpha 2,3 linked sialic acids appear often in healthy functioning cells. In cancer cells, glycans on the surface often have overexpressed alpha 2,6 linked sialic acids which aids in their metastasis and tumor progession. Sialic acids are also post translationally modified even further with acetate groups. Depending on where an acetate group is added, it can promote tumor progression, or in the opposite direction, promote apoptosis.

Many, many, many proteins are glycosylated, and contain one, two, several, or many more different types of glycoforms (that is they contain differently linked structures at the same sites of glycosylation) that change how they work, how much is expressed in places likes the cell surface, or where they are trafficked.

Another simple example is the difference between cellulose and starch. Everyone knows how the biology of two glucoses added together changes simply on how they're arranged. Now imagine complex tree like glycan structures decorating a vast number of proteins that can potentially change their linkages and structures and alter the way the proteins function or where they go. The genome is quite small, but how does life create many more functioning proteins than what can seemingly be encoded by the genome? Well PTMs like glycosylation are a big part of the reason why.

PTMs can not be controlled or predicted easily like DNA can. It's simply not template driven and dynamically responds to environment. What's even more frustrating is the microheterogenities it creates. The same proteins can be glycosylated differently at the same exact sites in different cell populations which changes how those same proteins function or how much might be expressed on different cell surfaces.

Just because one might be able to control DNA doesn't mean that one can create a properly functioning cell when everything from environment to cell-cell communication and uncontrollable (at least for now) PTMs are going to change the final output. It's science though, nothing should ever be ruled impossible. One day we might be able to create life from scratch, but we'll loooonnng be dead.
 
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  • #55
The large number of different possible outcomes from simple changes just reinforces the idea that not a lot of complexity is needed to kickstart things - the complex outcomes are built-in to the simple rules at the start.

The trick is not to let the complexity overwhelm you.
 
  • #56
Simon Bridge said:
The large number of different possible outcomes from simple changes just reinforces the idea that not a lot of complexity is needed to kickstart things - the complex outcomes are built-in to the simple rules at the start.

The trick is not to let the complexity overwhelm you.

That reminds me of Go. simple rules but the complexity is great :)
 
  • #57
In fact, Go has been used to study complexity. One of the intreguing things about Go is to see if a thrid party could figure out the rules of the game just from watching the play.

By extension: cellular automata.
 
  • #58
gravenewworld said:
Ah but different arrangements do lead to different results. How about a simple example? Sialic acids are carbohydrates that often cap the ends of glycan structures. Alpha 2,3 linked sialic acids appear often in healthy functioning cells. In cancer cells, glycans on the surface often have overexpressed alpha 2,6 linked sialic acids which aids in their metastasis and tumor progession. Sialic acids are also post translationally modified even further with acetate groups. Depending on where an acetate group is added, it can promote tumor progression, or in the opposite direction, promote apoptosis.
Well, where does that change in cancer cells come from? If a DNA mutation is the source, we are back to DNA again.

The only mention of "single [anything]" I see is "A single copy of the OGT gene is located on the X chromosome in humans and mice and OGT gene deletion in mice was embryonically lethal, demonstrating that OGT activity/O-glycosylation is vital for life [21].", indicating that those molecules are generated based on DNA sequences.

Just because one might be able to control DNA doesn't mean that one can create a properly functioning cell when everything from environment to cell-cell communication and uncontrollable (at least for now) PTMs are going to change the final output. It's science though, nothing should ever be ruled impossible. One day we might be able to create life from scratch, but we'll loooonnng be dead.
I am sure the first artificial biological life will be a very simple unicellular organism, and probably very similar to an existing natural cell. Probably more like a copy than a completely new design.
 
  • #59
Prions offer an abiogenetic path for creating new organic molecules, IMO.
 
  • #60
It's just plain silly to think that a protein could form by chance. No one thinks it could so would good does it do to prove it could not happen. Proteins evolved loved from simpler molecules.

The first life was based on RNA and was VERY simple. It likely did not even use proteins and just make everything out of RNA. It was not even really what we'd call "life" Just mildly self-replicating. Life was easy back then as there was no competition from other living things. The first "cell" may have lacked a cell membrane Proteins would have come later, after RNA

I'd say "never in the Universe even once did a protein ever form by chance. Always in every case there was RNA first. Later DNA evolved as a stronger form of storage. But the sequence is and always was RNA, then protein.
 

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