Can we create life from scratch?

[DiracPool]

Don't you agree?

https://www.youtube.com/watch?v=S8ecCnn5o1o

 

[Jon_Trevathan]

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.

 

[Borek]

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.

 

[DiracPool]

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

 

[Jon_Trevathan]

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?"

 

[SW VandeCarr]

. 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.

 

[Simon Bridge]

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.

 

[berkeman]

Thread closed temporarily for Moderation...

EDIT -- Thread re-opened. Thread is being monitored by the Mentors.

 

[SW VandeCarr]

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

 

[Jon_Trevathan]

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 = n^s [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 = (v_s + v_s+1 + v_s+2 + ... + v_s(max) ) ÷ (t_s + t_s+1 + t_s+2 + ... + t_s(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.

 

[DiracPool]

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.

 

[Detached]

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.

 

[gravenewworld]

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...

 

[DiracPool]

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.

 

[Simon Bridge]

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.

 

[Chronos]

I think prions are a great clue how nature may have managed the feat of abiogenesis.

 

[DiracPool]

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.

 

[mfb]

@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.

 

[gravenewworld]

@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.

 

[Simon Bridge]

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.

 

[Tenshou]

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 :)

 

[Simon Bridge]

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.

 

[mfb]

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.

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 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.

 

[Chronos]

Prions offer an abiogenetic path for creating new organic molecules, IMO.

 

[ChrisJA]

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.

 

[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.