DNA Self Assembly, Abiogenesis and How Science REALLY Works

This article appeared today in Science Daily. I thought it very timely and decided to post it here for the benefit of those interested in real science and for those who have bought in to Creationism (you know who you are) and have a hard time getting up in the morning (because you don't like to work and can't handle the truth). If you're interested in "origins", then this paper is for you.

New study hints at spontaneous appearance of primordial DNA

April 7, 2015

University of Colorado at Boulder


Summary:

The self-organization properties of DNA-like molecular fragments four billion years ago may have guided their own growth into repeating chemical chains long enough to act as a basis for primitive life, says a new study.



"The new research demonstrates that the spontaneous self-assembly of DNA fragments just a few nanometers in length into ordered liquid crystal phases has the ability to drive the formation of chemical bonds that connect together short DNA chains to form long ones, without the aid of biological mechanisms. Liquid crystals are a form of matter that has properties between those of conventional liquids and those of a solid crystal -- a liquid crystal may flow like a liquid, for example, but its molecules may be oriented more like a crystal.

"Our observations are suggestive of what may have happened on the early Earth when the first DNA-like molecular fragments appeared," said Clark."

www.sciencedaily.com...

This is not the first time that self assembly has been observed - it has been observed in atoms that make up the fundamental building blocks of molecules associated with living organisms like nucleic acids, in RNA and numerous other molecules.

The original paper which appeared in Nature Communications:

Abiotic ligation of DNA oligomers templated by their liquid crystal ordering
Tommaso P. Fraccia, Gregory P. Smith, Giuliano Zanchetta, Elvezia Paraboschi, Yougwooo Yi, David M. Walba,Giorgio Dieci, Noel A. Clark
& Tommaso Bellini

Nature Communications 6, Article number: 6424 doi:10.1038/ncomms7424 Received 20 November 2014 Accepted 28 January 2015 Published 10 March 2015


Discussion

"In the formulation of origin-of-life scenarios, self-assembly is often invoked15, 16 as the only available mechanism to bridge the ‘insurmountable kinetic barrier’17 connecting simple carbon-based molecules available on the early Earth and the simplest structures capable of enzymatic activity18, which in a RNA world scenario would be ribozymes19, 20. Here we have offered a real example, based on DNA but very likely extendable to RNA3 or other nucleic acid precursors21, of how this path could have actually taken place, showing that the interplay of fluid ordering, aqueous phase separation, and distinctive modes of hierarchical and sequence-directed self-assembly can direct chemical reaction in a way that facilitates production of long chains of variable sequence. We envision our findings as a paradigm of what could have happened in the prebiotic Earth based on the fundamental and simplifying assumption that the origin of nucleic acids is written in their structure. This vision combines well with the classic notions of thermal and drying–wetting cycles, generally considered basic drivers for life to emerge on early Earth22, 23, and with more recent notions such as the thermophoretic accumulation of DNA-like molecules in hydrothermal pore systems24, 25, thereby offering a plausible pathway for the molecular crowding crucial for LC ordering to appear."

www.nature.com...



This is how real science is done - it is not the chaotic rhetoric of Creationists who have zip hard evidence to support their claims.

a reply to: Phantom423

Fascinating stuff.
We really are on the verge of discovering how life began.
Thats gonna scare many so expect the usual religious crowd to chime in and deny science and expect some bleating we shouldn't play god.
Personally I think god will be well chuffed to know how far we have come and how much we have discovered.

Interesting research.

Phase dependent production suggests 'intelligent DNA' acting upon catalysts.

There is obvious mention of ''when DNA like molecular fragments appeared on Earth.. or it could have been complete DNA, either way, as with all atoms it arrived from space. There is then the hypothesis that DNA (fragmentary or otherwise) arrived with this intelligence, inherently pre programmed to act upon catalyst states.

Interesting the catalyst states are liquid and crystalline, crystals are interesting, there is research showing DNA interactions with metal ions alters the geometric structure of the DNA.

Also interesting is the description of hierarchical structures, in a micro /macrocosm way it could be society as a reflection of DNA.

structbio.vanderbilt.edu...

"Our observations are suggestive of what may have happened on the early Earth when the first DNA-like molecular fragments appeared," said Clark."

showing that the interplay of fluid ordering, aqueous phase separation, and distinctive modes of hierarchical and sequence-directed self-assembly can direct chemical reaction in a way that facilitates production of long chains of variable sequence.

a reply to: Phantom423

Wow credible science for once. Just wait, before long a Creationist will be along to dismiss it completely without reading and understanding any of the science.

Although I believe what they are saying is true, you have to take a few things into consideration. First of all the frequency of this planet, tied to life being present on it, is involved in the results of what they are seeing. Now this frequency, created by life itself, was not present in the beginning of this world unless it was transported from somewhere else. DNA interacts with frequency, change the frequency and the results are altered, meaning assembly would be different and the results obtained might not be viable. Even crystal formation interacts with frequency present. The energy signature of this planet is directly related to all things on it, including life itself.

Now this is just my interpretation based on reading a lot of articles and thinking about the subject a lot. I have no evidence to back what I say, but parts of this are included in many scientific research articles scattered all over the place.

Also, the ability to create consciousness is way more complex than what they are talking about. Even a tree has consciousness, even bacteria and fungi have collective consciousness.

Very interesting research, and it points that fast life growth of Cambrian explosion is very much possible.

originally posted by: rickymouse
Also, the ability to create consciousness is way more complex than what they are talking about. Even a tree has consciousness, even bacteria and fungi have collective consciousness.

Do atoms have 'consciousness' and what is difference between 'consciousness' and 'collective consciousness'??

Sorry, but this just has huge 'Deepak Chopra' label over it...

So as not to disappoint,

They didn't prove anything it is just a bunch of "mays" and "could haves".
Just more text for the religion of science.

Carry on.

originally posted by: TinfoilTP
So as not to disappoint,

They didn't prove anything it is just a bunch of "mays" and "could haves".
Just more text for the religion of science.

Carry on.

Maybe you should write them a letter and tell them to retract the article because it "didn't prove anything". You obviously don't know how to read a research article which is fine. But you're drawing a conclusion based...... on what again?????

originally posted by: TinfoilTP
So as not to disappoint,

They didn't prove anything it is just a bunch of "mays" and "could haves".
Just more text for the religion of science.

Carry on.

Certainty is something you will find in religion. Honesty is what you will find with science.

originally posted by: rickymouse
Although I believe what they are saying is true, you have to take a few things into consideration. First of all the frequency of this planet, tied to life being present on it, is involved in the results of what they are seeing. Now this frequency, created by life itself, was not present in the beginning of this world unless it was transported from somewhere else. DNA interacts with frequency, change the frequency and the results are altered, meaning assembly would be different and the results obtained might not be viable. Even crystal formation interacts with frequency present. The energy signature of this planet is directly related to all things on it, including life itself.

Now this is just my interpretation based on reading a lot of articles and thinking about the subject a lot. I have no evidence to back what I say, but parts of this are included in many scientific research articles scattered all over the place.

Also, the ability to create consciousness is way more complex than what they are talking about. Even a tree has consciousness, even bacteria and fungi have collective consciousness.

Well the article stands on its own merits. Of course there are a lot more questions and speculation. We don't understand what consciousness really is - but it's a good question - remember we still have the quantum world to deal with in all this. Life isn't just what we perceive in our daily living or even in the lab. We have an entire "underground economy" so-to-speak that we don't see. So all that will have to be factored in as well. A long journey, but an interesting one.

a reply to: Phantom423

If we knew everything about everything, this place would be pretty boring. Nobody would make a mistake and we wouldn't have anything to chuckle about. Science would not be needed since we would know everything and everything would be boring as hell because we would not need to learn the truth. Searching for answers is one of my favorite pastimes. I have to weed through hundreds of articles containing misconceptions and half truths cut by Occams Razor over generations to figure out things. I have to try to understand what motivated research in the first place and the parameters of the research.

Then you find out something and feel so good and google the conclusion only to find someone has already found that out but nobody listened to what they were saying.

Oh well, I suppose if there was an ignore button here, people would always press it on me and I would be the only one to see what I wrote. Everyone seems to want to reinforce their beliefs. Once I started studying I thrashed my beliefs and no longer believe that half of the supposedly proven things are real. You can believe the research if you understand the reason the research was done and the things they did not test. Most of the misinterpreted info is generated either for monetary gain or desire for recognition. That doesn't matter though, lots of stuff done for gain is actually real but sometimes the parameters make it useless overall and the information is inadequate because of this.

Still I read lots of research going to the source for the proper information including the things that limit it's usability. It's what we got and it is better than nothing.

originally posted by: Krazysh0t
a reply to: Phantom423

Wow credible science for once. Just wait, before long a Creationist will be along to dismiss it completely without reading and understanding any of the science.

Come on, man... didn't you see all those big hard-to-pronounce words? You expect anyone to actually read and comprehend that nonsense?

Yes, this is the point I've arrived at thanks to dealing with the mush-brained minority on ATS.

originally posted by: Phantom423

originally posted by: TinfoilTP
So as not to disappoint,

They didn't prove anything it is just a bunch of "mays" and "could haves".
Just more text for the religion of science.

Carry on.

Maybe you should write them a letter and tell them to retract the article because it "didn't prove anything". You obviously don't know how to read a research article which is fine. But you're drawing a conclusion based...... on what again?????

Prepare for...

a reply to: Answer

Made more sense than the usual stiff they bleat did that pic.

Lets examine this mass of text that uses long lofty sounding words.

"In the formulation of origin-of-life scenarios, self-assembly is often invoked15, 16 as the only available mechanism to bridge the ‘insurmountable kinetic barrier’17 connecting simple carbon-based molecules available on the early Earth and the simplest structures capable of enzymatic activity18, which in a RNA world scenario would be ribozymes19, 20. Here we have offered a real example, based on DNA but very likely extendable to RNA3 or other nucleic acid precursors21, of how this path could have actually taken place, showing that the interplay of fluid ordering, aqueous phase separation, and distinctive modes of hierarchical and sequence-directed self-assembly can direct chemical reaction in a way that facilitates production of long chains of variable sequence. We envision our findings as a paradigm of what could have happened in the prebiotic Earth based on the fundamental and simplifying assumption that the origin of nucleic acids is written in their structure. This vision combines well with the classic notions of thermal and drying–wetting cycles, generally considered basic drivers for life to emerge on early Earth22, 23, and with more recent notions such as the thermophoretic accumulation of DNA-like molecules in hydrothermal pore systems24, 25, thereby offering a plausible pathway for the molecular crowding crucial for LC ordering to appear."

scenarios, invoked, offered, very likely, could have, we envision, paradigm, what could have happened, assumption, vision, notions, generally considered, recent notions, plausible.

Walk through that gibberish and find each and every one of those bonding it all together.

If that is supposed to be a shining example of science, somebody needs to eat their shorts.

a reply to: rickymouse

Adding this video since it discussed the possibility of quantum tunneling being a possible solution for mutation.


Consciousness as a quantum effect.

originally posted by: TinfoilTP
Lets examine this mass of text that uses long lofty sounding words.

I'm so glad it was you who came here to prove my point about long, hard-to-pronounce words.

As with all other scientific topics, your misunderstanding of the data being presented is irrelevant to the validity of said data.

a reply to: TinfoilTP

By "lofty sounding" you mean tecnically appropriate terms? Its not sciences fault that you feel excluded from this. Science will be honest, science will reevaluate its theories based on evidecne. As I said, it is called honesty. Its also a lifescience paper, you are not going to get an answer of 1.25 daltons. It is not how that works.

So, in spite of all the namby pamby words and suchlike we have here a hypothesis. I like hypotheses, as they can be proven or refuted on the basis of experiment and result. Nice one OP. S+F

originally posted by: Jonjonj
So, in spite of all the namby pamby words and suchlike we have here a hypothesis. I like hypotheses, as they can be proven or refuted on the basis of experiment and result. Nice one OP. S+F

The results are real results. Results are not a hypothesis. If DNA self assembly was a hypothesis, then this paper collapsed that hypothesis as it is now fact.