Can we create life from scratch?

[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.

 

[humbleteleskop]

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

Do we have any reason to believe abiogenesis ever ceased and that is not happening even today?

 

[mfb]

All known species use the same genetic code to translate DNA/RNA to amino acids (sometimes with tiny modifications). If there would have been completely independent evolutions, we would see many different ways.
Life needed a long time to get as competitive as today. I doubt new life would have any chance to survive against current life - it just lacks billions of years of evolution.

 

[humbleteleskop]

All known species use the same genetic code to translate DNA/RNA to amino acids (sometimes with tiny modifications). If there would have been completely independent evolutions, we would see many different ways.
Life needed a long time to get as competitive as today. I doubt new life would have any chance to survive against current life - it just lacks billions of years of evolution.

I would expect abiohenesis of today would be based on the same principles, guided and limited by the same or similar external factors, so I don't think it would be able to produce anything fundamentally different, on this planet.

Simple self-replicating molecules could have an advantage of being more robust and existing in large quantities. I'm not suggesting it would be possible for flying snake to evolve in today's and the world of tomorrow, but perhaps a new virus, very much similar to those that already exist, yet not quite the same. Of course it would be hard or impossible to tell whether this virus is just a mutation or indeed evolved from something simpler than itself.

 

[Ryan_m_b]

Do we have any reason to believe abiogenesis ever ceased and that is not happening even today?

It's unlikely abiogenesis is still ongoing because extant organisms are likely to fill any niche where it could occur.

 

[ChrisJA]

Do we have any reason to believe abiogenesis ever ceased and that is not happening even today?

The theory is that if some new kind of life sprang up it would be VERY poor at competing for resources and in fending off the more advanced microbes that would see it as food.

Also, before there was life on Earth, the Earth was a different place. There was no O2 in the atmosphere and so on. The lifeless Earth was a better place for life to develop but now the air is reactive (with O2) and the nutrient-soup is gone.

Life might have arisen many times only to fail until finally life RNA based on four bases happened and then we had RNA based life for a billion years before DNA came along. The first life to survive and multiply "wins" and would prevent anything else from following. It changes the environment so radically while at the same time adapting to the changes, nothing else can follow it

 

[humbleteleskop]

I agree. However, if something like those self-replicating polymers and fatty acids from Szostak's experiments can occur naturally in large numbers and in an environment sparse or devoid from things that would consume them. Then they could perhaps merge just due to sheer luck and consequently divide like in the experiment.

And then, maybe, just maybe, some of them would turn into something a little bit more robust, something a little bit more likely to merge and divide, and so on... Perhaps at some point external factors would not allow for any further grow in complexity, but it's just a matter of our semantic definition whether we are willing to call those things "alive".