Can we create life from scratch?

[Borek]

The first life was based on RNA

This is just one of possible answers, not a definitive one, as you make it sound.

 

[Fermifaq]

Self-assembly
http://en.wikipedia.org/wiki/Self-assembly

 

[Fermifaq]

Simple Artificial Cell Created From Scratch To Study Cell Complexity
http://www.sciencedaily.com/releases/2008/05/080515171023.htm

Similar efforts have been made by numerous other research teams and we are rapidly acquiring the tools to build a complete cell from scratch.

FIRST SELF-REPLICATING SYNTHETIC BACTERIAL CELL Frequently Asked Questions
http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/faq

With on going incremental advances it is highly likely we will be able to build a complete cell 100% from scratch by the end of this century. Currently most efforts still borrow heavily from living organisms.

 

[lisab]

It is quite likely that numerous lifelike systems emerged in many locations, many times and continued to do so for millions of years...

Early life was probably very fragile and inefficient, it is highly likely that many symbiotic relationship where formed...

While one cannot rule out a single very lucky complex event it is far more likely that 'life like things' emerged and became extinct time and again over periods of millions of years...

Today's single celled organisms are almost certainly far more hardy and efficient than early life...

In the media you will often hear undersea vents being cited as a possible source for the origin of life. This is almost certainly nonsense as the 'chemical freedoms' in such environments far out weigh the 'chemical constraints',so it would be like trying to paint a Van goh in in a typhoon...

Fermifaq, we have a hard-and-fast rule here about speculation. Before you post again please back up these statements with mainstream (i.e., peer-reviewed) sources.

 

[Jon_Trevathan]

The potential for self-replication makes RNA an attractive candidate as a primordial catalysis in the origin of life. Catalysis may have occurred in some kind of compartment, possibly a fatty acid vesicle. However, RNA catalysis generally requires high levels of magnesium, which are incompatible with fatty acid vesicle integrity. Adamala and Szostak (p. 1098) screened magnesium chelators and found that several—including citrate, isocitrate, and oxalate—could maintain the membrane stability of fatty acid vesicles in the presence of Mg2+. Citrate also allowed Mg2+-dependent RNA synthesis within protocell-like vesicles, while at the same time protecting RNA from Mg2+-catalyzed degradation.
http://www.sciencemag.org/content/342/6162/1098

 

[boymilk]

The "Spiegelman Monster" was the name given to a short devolved RNA strand consisting of ~200 to ~50 bases that replicated itself very quickly in the presence of Q-Beta replicase in a process similar to that of the polymerase chain reaction (which uses DNA instead of RNA):

http://www.ncbi.nlm.nih.gov/pubmed/5217468

The research itself is quite old now but what is perhaps most intriguing is the following:

"M. Sumper and R. Luce of Eigen's laboratory demonstrated that a mixture containing no RNA at all but only RNA bases and Q-Beta Replicase can, under the right conditions, spontaneously generate self-replicating RNA which evolves into a form similar to Spiegelman Monster."

http://www.ncbi.nlm.nih.gov/pubmed/1054493

Chemical networks of interacting RNA molecules, autocatalytic and non-autocatalytic RNA ribozymes, and (possibly) proteins, perhaps contained within lipid vesicles, could have led to the development of self-reinforcing hypercycles of increasing complexity and efficiency due to Darwinian evolution and the first proto-cells.

Also this is very interesting:

"Lincoln and Joyce developed an RNA enzyme system capable of self-replication in about an hour. By utilizing molecular competition (in vitro evolution) of a candidate enzyme mixture, a pair of RNA enzymes emerged, in which each synthesizes the other from synthetic oligonucleotides, with no protein present."

http://www.ncbi.nlm.nih.gov/pubmed/19131595

Anybody who is interested in abiogenesis and synthetic biology should also check out Jack Szostak's work here and his basic introduction to the subject here.

 

[Simon Bridge]

The difficulty of defining "life" is usually central to this sort of discussion ... how would you know it if you had it? Is the Speigelman Monster alive?

"When chemistry becomes life" would form fundamental research in both fields right?

For a physicist, the distinction would be meaningless except that we seem to be made up of the living stuff - and continuing to do physics seems to depend on applied biology maintaining the process of life.

 

[ndjokovic]

I think to be able to create a cell, we must first master physics and mathematics, specially quantum physics.
Let's take for example this molecular machine inside our body:

https://www.youtube.com/watch?v=PjdPTY1wHdQ This machine is made of 2062 amino acid molecules. Covalent bond and hydrogen bonds is what makes these molecules joined (electric forces). This machine is not constructed like this in the first time, but it is constructed by another machine called Ribosome in the form of string of molecules, then this string of molecules fold because of electric forces into parts which then make the working machine. But the whole process takes only nanoseconds:

https://www.youtube.com/watch?v=TfYf_rPWUdY

A small machine of only 100 amino acids molecules can take some 10¹⁰⁰ different configurations to fold. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Biologists now don't have an idea just how these molecules fold in nanoseconds. Only quantum physics can explain this phenomenon:
http://link.springer.com/article/10.1007/s11433-014-5390-8

In the recent 3 years, quantum physics is becoming more and more interesting in biology, since the discovery of the "spooky action at a distance" in migrating birds:

https://www.youtube.com/watch?v=jepgOQEvWT0
and in plants:
http://www.kurzweilai.net/evidence-that-photosynthesis-efficiency-is-based-on-quantum-mechanics

There's also a recent discovery of quantum vibrations in 'microtubules' inside brain neurons:
http://www.sciencedaily.com/releases/2014/01/140116085105.htm

We also should master the dynamics of molecules to be able to make molecular machines working with great accuracy inside a storm of Brownian motion of water molecules:

https://www.youtube.com/watch?v=bee6PWUgPo8

Now imagine if those machines are exposed to radiation, a single photon hit some atom in these machines, and cause some electron to leave the atom, the charge of atom will change which will make it "stick" to other atoms causing the whole machine to collapse, and this can make some random electric attractions between other machines. The cell has a system of other machines that fight those random mutations and detect which machine is working and which one is not working.All these machines should be put to work together with high accuracy and without conflicts to form the big factory which is the cell.

So, building machines in the nanoscopic scale is far more complex then the macroscopic scale, because, new forces are added to the equations like: the mighty electric forces, Brownian motions of molecules, and the quantum phenomenon.

 

[Ygggdrasil]

This machine is made of 2062 amino acid molecules. Covalent bond and hydrogen bonds is what makes these molecules joined (electric forces). This machine is not constructed like this in the first time, but it is constructed by another machine called Ribosome in the form of string of molecules, then this string of molecules fold because of electric forces into parts which then make the working machine. But the whole process takes only nanoseconds:

Protein folding does not take place on the nanosecond timescale. First, ribosomes synthesize proteins at a rate of about 10-20 amino acids per second (http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=100059&org=%), so synthesizing a ~2000 amino acid enzyme would take at least ~100 seconds, and folding occurs during synthesis. Even in artificial studies of protein folding (e.g. laser temperature jump studies), the folding rates of the fastest folding proteins are on the order of microseconds (although individual elements of the protein can probably become structured on the tens-hundreds of nanoseconds timescale) (see Kubelka, Hofrichter and Eaton. 2004. The protein folding ‘speed limit’. Curr Opin Struct Biol 14: 76. http://dx.doi.org/10.1016/j.sbi.2004.01.013 ).

A small machine of only 100 amino acids molecules can take some 10¹⁰⁰ different configurations to fold. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Biologists now don't have an idea just how these molecules fold in nanoseconds. Only quantum physics can explain this phenomenon

How proteins fold without having to sample all possible configurations (Levinthal's paradox) is a solved problem. Proteins have evolved to have a "funnel-shaped" energy landscape, such that the energetics of their interactions will guide them toward the correct, native structure (see, for example, Dill and MacCallum 2012. The Protein-Folding Problem, 50 Years On. Science 338:1042. doi:10.1126/science.1219021). Furthermore, it is not necessary to use quantum mechanics to explain protein folding as computer simulations based on only classical physics can model protein folding very well (Lindorff-Larsen et al. 2011. How Fast-Folding Proteins Fold. Science 334: 517 doi:10.1126/science.1208351) (in fact, we understand the folding of fast-folding proteins much better than we do the folding of slow-folding proteins).

In the recent 3 years, quantum physics is becoming more and more interesting in biology, since the discovery of the "spooky action at a distance" in migrating birds:
and in plants:
http://www.kurzweilai.net/evidence-that-photosynthesis-efficiency-is-based-on-quantum-mechanics

These are two good examples of processes where quantum mechanics is important for understanding biological phenomena.

There's also a recent discovery of quantum vibrations in 'microtubules' inside brain neurons:
http://www.sciencedaily.com/releases/2014/01/140116085105.htm

And this, in my personal and professional opinion, is complete and utter ********.

 

[ndjokovic]

Protein folding does not take place on the nanosecond timescale. First, ribosomes synthesize proteins at a rate of about 10-20 amino acids per second (http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=100059&org=%), so synthesizing a ~2000 amino acid enzyme would take at least ~100 seconds, and folding occurs during synthesis. Even in artificial studies of protein folding (e.g. laser temperature jump studies), the folding rates of the fastest folding proteins are on the order of microseconds (although individual elements of the protein can probably become structured on the tens-hundreds of nanoseconds timescale) (see Kubelka, Hofrichter and Eaton. 2004. The protein folding ‘speed limit’. Curr Opin Struct Biol 14: 76. http://dx.doi.org/10.1016/j.sbi.2004.01.013 ).

I am sorry because I meant by the "whole process" only the folding, not the work done by the Ribosome.

How proteins fold without having to sample all possible configurations (Levinthal's paradox) is a solved problem. Proteins have evolved to have a "funnel-shaped" energy landscape, such that the energetics of their interactions will guide them toward the correct, native structure (see, for example, Dill and MacCallum 2012. The Protein-Folding Problem, 50 Years On. Science 338:1042. doi:10.1126/science.1219021). Furthermore, it is not necessary to use quantum mechanics to explain protein folding as computer simulations based on only classical physics can model protein folding very well (Lindorff-Larsen et al. 2011. How Fast-Folding Proteins Fold. Science 334: 517 doi:10.1126/science.1208351) (in fact, we understand the folding of fast-folding proteins much better than we do the folding of slow-folding proteins).

But there's still the problem of the nonlinear and asymmetric relation between folding/unfolding and temperature which those models can't explain.

Besides the quantum techniques used by plants and birds, I just want to mention the need of a better understanding of quantum physics, to understand better the 3d shapes of molecular machines which is controlled by the hydrogen bonds which is also based on quantum mechanics. The quantum behavior of electrons around hydrogen and oxygen can result in a either weakening or strengthening of the hydrogen bond which affects the way the protein folds.

And this, in my personal and professional opinion, is complete and utter ********.

The discovery of quantum vibrations in the brain is fact. I think you may disagree with the theory that gains a support with this discovery, but that's not how you should talk about it. I am not a supporter of this theory, I need more information to judge it. But if we want to attack it, we should find some weaknesses. Einstein didn't like quantum physics, he saw it as a nonsense theory, but experiments proved Einstein was wrong. A thing like for example Delayed Choice Quantum Eraser can sound weird and nonsense, but it is fact and proved by experiments.

 

[mfb]

The discovery of quantum vibrations in the brain is fact. I think you may disagree with the theory that gains a support with this discovery, but that's not how you should talk about it. I am not a supporter of this theory, I need more information to judge it. But if we want to attack it, we should find some weaknesses. Einstein didn't like quantum physics, he saw it as a nonsense theory, but experiments proved Einstein was wrong. A thing like for example Delayed Choice Quantum Eraser can sound weird and nonsense, but it is fact and proved by experiments.

I don't even see how the theory would gain support by those vibrations. It is obvious that quantum mechanics is valid in the brain (otherwise chemistry would not work), but you would have to prove that it is relevant for the way the brain works. And even if that is done, I don't see a special relation to consciousness. There are many things that influence how the brain works, why would you pick one of them and see something special about it?

 

[Ryan_m_b]

This conversation is trending towards quantum mind theories (which attract a lot of pseudoscience and are by no means mainstream) and philosophy. Please stick to the topic at hand concerning synthetic biology.

 

[epenguin]

Probably many many times 3.5-4.5 billion years ago... and wait for a long long time ;)

That would be the definition of "enough time" then wouldn't it?
You don't get to go backwards all that much though so once on a path, events have to continue along it.
How many times would you have to roll a fair die before it is certain that you will roll at least one six?

The rest of these terms are vague: what is "luck"? How would you recognize it if you saw it? Destiny?

In AD&D you have to generate characters by rolling 3 dice and adding the total. But there are gamer tricks to get a higher value while keeping the actual number random ... eg - one rolls 4 dice, reroll the 1s and discard the lowest.
So, in this example, on the first roll I get 5,5,1,1 ... now the odds have changed - I cannot get less than an 12 for that attribute, because some dice rolled high that time. It could have been different? Was it fate? Was it an accidental sequence of events?

What is the "right" sequence of molecules? We happen to think that the RNA-DNA etc stuff is important because we are made of it ... but isn't that is just our own arrogance in thinking we are important? Why can't the "right" sequence be the one that leads to alcohol and all the rest is wrong? The only meaning to these events is what we assign to them.

Perhaps there are other sequences that lead to other kinds of self-replication that can develop the kind of complexity we normally associate with what we please ourselves to call "life"? Just 'cause we have it does not mean it's the only way. There is no way of knowing, yet, and detailed speculation is pointless. The point: let's not get up ourselves eh? The Universe still has a lot to teach us.

What is clear is that, in this "big" "old" Universe, there is enough room and time for many apparently unlikely things to happen. That's the thing about probability - the odds of an outcome change with the number of opportunities to roll the dice - and how the dice are rolled.

I think there is a misconception in this and other posts in the idea that it is very difficult to to get life started. There has been life on Earth for most of the time there has been an Earth capable of harbouring it. Last I heard there has been life for at least 5 of the 5.3 billion years of Earth history. At least - it might have started within the first 10.000 years for all we know.

In saying many X5 billion years you are presumably appealing to the 'seeding' concept, seeding by spores or seeds from astronomically distant places. This (quite old) hypothesis is very little regarded amongst OOL people today. Apart from its relative sterility as research project and its pushing back rather than trying to deal with the problem (yet the same problem remains even when you push it back) you get into the same large improbabilities that made you take refuge in it, involving the size of the Universe and survival and arrival probabilities.

 

[Ygggdrasil]

But there's still the problem of the nonlinear and asymmetric relation between folding/unfolding and temperature which those models can't explain.

I believe this issue has been explained in the literature:

The anomalous temperature dependence of protein folding has received considerable attention. Here we show that the temperature dependence of the folding of protein L becomes extremely simple when the effects of temperature on protein stability are corrected for; the logarithm of the folding rate is a linear function of 1/T on constant stability contours in the temperature–denaturant plane. This convincingly demonstrates that the anomalous temperature dependence of folding derives from the temperature dependence of the interactions that stabilize proteins, rather than from the super Arrhenius temperature dependence predicted for the configurational diffusion constant on a rough energy landscape.​

Scalley and Baker. 1997. Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proc. Natl. Acad. Sci. USA. 94: 10636. doi:10.1073/pnas.94.20.10636.

Besides the quantum techniques used by plants and birds, I just want to mention the need of a better understanding of quantum physics, to understand better the 3d shapes of molecular machines which is controlled by the hydrogen bonds which is also based on quantum mechanics. The quantum behavior of electrons around hydrogen and oxygen can result in a either weakening or strengthening of the hydrogen bond which affects the way the protein folds.

Here, I agree with you. If a better understanding of quantum mechanics can improve our understanding of hydrogen bonding in proteins, these insights will be very helpful in advancing our understanding of protein folding.

 

[Ophiolite]

I think there is a misconception in this and other posts in the idea that it is very difficult to to get life started. There has been life on Earth for most of the time there has been an Earth capable of harbouring it. Last I heard there has been life for at least 5 of the 5.3 billion years of Earth history. At least - it might have started within the first 10.000 years for all we know.

1. The Earth is 4.54 billion years old.
2. The oldest evidence for life (which is, however, disputed) is a chemical signature dating to 3.7 Ga, in Greenland.
3. The oldest solid evidence for life consists of stromatolites dated at 3.5 Ga.
4. Frequent high energy impacts would have sterilised the planet had any life formed at an early stage.

 

[Simon Bridge]

Naturally I would not want anything I wrote to be construed to mean anything else.

i.e. re: http://paleobiology.si.edu/geotime/main/htmlversion/archean3.html
... which suggests life is likely everywhere or that places like the Earth are particularly favored flukes.

The trouble comes from arguments that evolution and known Laws of Nature make Life unlikely - and yet life happened on Earth as soon as Earth could support it. If you spend a lot of time around evolutionists you get sick of it.

Thing is - we need not assume life is likely to get life somewhere.

 

[Ophiolite]

To extrapolate from a sample size of one shows poor judgement.

 

[ndjokovic]

It is obvious that quantum mechanics is valid in the brain (otherwise chemistry would not work)

I just want to mention a fundamental misunderstanding here, I am not talking about quantum phenomenon which is present in every atom of the universe, but I am talking about quantum techniques used by some living organisms, like this:

https://www.youtube.com/watch?v=jepgOQEvWT0 and used also in photosynthesis.

 

[mfb]

It is obvious that quantum mechanics is valid in the brain (otherwise chemistry would not work)

I just want to mention a fundamental misunderstanding here, I am not talking about quantum phenomenon which is present in every atom of the universe, but I am talking about quantum techniques used by some living organisms, like this:

You quoted that part completely out of its context.

It is obvious that quantum mechanics is valid in the brain (otherwise chemistry would not work), but you would have to prove that it is relevant for the way the brain works.

 

[ndjokovic]

I don't even see how the theory would gain support by those vibrations. It is obvious that quantum mechanics is valid in the brain (otherwise chemistry would not work), but you would have to prove that it is relevant for the way the brain works. And even if that is done, I don't see a special relation to consciousness. There are many things that influence how the brain works, why would you pick one of them and see something special about it?

You quoted that part completely out of its context.

First, I quoted the part where you misunderstood the problem. Second, as I explained before, I am not even a supporter of this theory, it is a theory that predicted the quantum vibrations of microtubules which got harshly criticized from its inception, as the brain was considered too "warm, wet, and noisy" for seemingly delicate quantum processes. But it turns out that the theory was right about those quantum vibrations, if you want to know how this theory explains how the brain works, you just have to read it. I didn't even read it, I am not even interested by this theory of consciousness. I am only interested with the discovery of such vibrations in the brain which are not obvious, contrarily to what you said.

 

[gravenewworld]

How does quantum mechanics have anything to do with biology that happens on a much larger scale (whole cell-tissue-organ-whole organism)? This is reductionism at its finest...when there have been many examples of where and how reductionism in biology has led to failure after failure (just look at the drug industry that tries to reduce problems down to simple canonical signaling pathways to identify targets for hitting with new drugs which has led to ever declining success ). QM and molecular dynamical simulations can barely model ligand-receptor binding, yet we're now trying to explain something as complex as the brain (let alone a single cell) through QM? This makes no sense. Biology is a whole different beast, and one does not need to understand every single molecular underpinning at a quantum level (which is practically impossible for the human mind to do anyway) to be able to do or understand biology.

 

[ndjokovic]

How does quantum mechanics have anything to do with biology that happens on a much larger scale (whole cell-tissue-organ-whole organism)? This is reductionism at its finest...when there have been countless examples of where and how reductionism in biology has led to failure after failure (just look at the drug industry that tries to reduce problems down to simple canonical signaling pathways to identify targets for hitting with new drugs which has led to ever declining success ). QM and molecular dynamical simulations can barely model ligand-receptor binding, yet we're now trying to explain something as complex as the brain (let alone a single cell) through QM? This makes no sense. Biology is a whole different beast, and one does not need to understand every single molecular underpinning at a quantum level (which is practically impossible for the human mind to do anyway) to be able to do or understand biology.

I think you should update your knowledge, there's even a field called Quantum Biology. I gave a couple of discoveries about that on my other comments.

 

[mfb]

First, I quoted the part where you misunderstood the problem.

No. You quoted some part which is
(a) true
(b) completely irrelevant without the second part.

And then you assumed I would have misunderstood something, which I did not.

I am only interested with the discovery of such vibrations in the brain which are not obvious, contrarily to what you said.

I did not say (or mean, or think) this.

 

[ndjokovic]

No. You quoted some part which is
(a) true
(b) completely irrelevant without the second part.

And then you assumed I would have misunderstood something, which I did not.
I did not say (or mean, or think) this.

Then I am sorry if you see that I misunderstood you, even if I kept reading your comment lot of times to make sure I get your point.

 

[Simon Bridge]

I suspect you meant something more like:

I [don't want anyone to think I am] talking about quantum phenomenon which is present in every atom of the universe, but I [want to fucus on] about quantum techniques used by some living organisms,...

By which you mean something like :
http://www.wired.com/wiredscience/2011/01/quantum-birds/
i.e. How quantum entanglement is postulated as playing an important role in the European Robin's navigation system.

When you see something like this in the pop-science, have a go looking at the literature: eg. http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.106.040503
... the clames are often not as sensational as the pop-science shows would make out.

More accessible (New Scientist), but slightly more sensational:
http://www.sciencedirect.com/science/article/pii/S0262407911601280

The role of QM in life on such a scale seems to be off-topic for this thread. I suspect that such approaches would end up in whatever organism ends up being artificially created shout that be possible. See subject line though.

Perhaps your interest in this topic is best pursued in another thread?
There you would be able to start out clean, being able to make careful statements about what it is exactly you want to talk about.

 

[Straw_Cat]

Hasn't this already been done, by some lab in Australia? From what I recall, they selected various strands of DNA, assembled them, and had a new life form. I don't remember which lab it was, sorry.

 

[Simon Bridge]

Hasn't this already been done, by some lab in Australia? From what I recall, they selected various strands of DNA, assembled them, and had a new life form. I don't remember which lab it was, sorry.

You may be thinking of
http://genetics.thetech.org/original_news/news75
(2008)

... but it was not "life from scratch" - they reproduced a bacterium genome by a process being described as "from scratch" but I don't think that's what post #1 means somehow.

There's also projects like:
http://onlinelibrary.wiley.com/doi/10.1002/anie.201105068/abstract
... inorganic chemical "cells" intended to, eventually, imitate organic biology.
Also see: http://www.gizmag.com/bringing-life-to-inoganic-matter/19855/

Australia gets mentoned a lot in connection with the introduction of new species because of the disasterous introduction of rabbits there. NZ has similar problems with Opossums, rabbits, rats,... mind you, introducing humans has been no picnic for the native wildlife either.

 

[ndjokovic]

The role of QM in life on such a scale seems to be off-topic for this thread. I suspect that such approaches would end up in whatever organism ends up being artificially created shout that be possible. See subject line though.

Perhaps your interest in this topic is best pursued in another thread?
There you would be able to start out clean, being able to make careful statements about what it is exactly you want to talk about.

I think I just mentioned the need of mastering at least quantum physics in order to be able to "create life from scratch", and I gave examples of organisms using quantum tricks. I don't see how this is off-topic. But you are right, the field of quantum biology needs its own topic. I am thinking about creating it one.

 

[Evo]

I think I just mentioned the need of mastering at least quantum physics in order to be able to "create life from scratch", and I gave examples of organisms using quantum tricks. I don't see how this is off-topic. But you are right, the field of quantum biology needs its own topic. I am thinking about creating it one.

Just remember that if you start a new thread, you need to first provide the peer reviewed research in an accepted journal, otherwise it will be deleted.

Notice how Simon, Ygggdrasil and other Science Advisors and Homework Helpers always link to proper sources, learn from them.

 

[Simon Bridge]

Well, assertions should be backed by such citations - but questions are just questions.

There are some intreguing effects that we resort to details of modern physics to explain:
like: how it is that L-protiens and D-sugars are what life uses. Stuff like that.
... may provide a place to start.

This is nitty-gritty stuff, looking for a reference found:
http://www.righthandlefthand.com/html/notes6.htm
(citations within and bibliography below)

But we can synthesize these things for use in our artificial life form without knowing why it is a good idea to do so. We may not need to use QM to make life, we need only that Nature knows how to use QM.