Creating life

[Bobsessed]

It may be silly, but I'm fascinated by the idea of creating something living out of non-living things.

has anybody ever made a cell out of non-living matter?

and can you make DNA?

 

sorry if this is dumb. I'm 16 and know nothing much about science but it does interest me.

 

I asked my chemistry teacher the second question and he said you can make proteins.. then he gave me a weird look, so i didn't ask him any more questions [science teachers have a way of making me feel very stupid]

[foofighter]

the only dumb question is that which doesn't get asked = ). Scientists recently succeeded in building the entire DNA sequence of a known species of bacteria, bit by bit, lego-style. The next goal is to put that DNA in a human-created cell membrane. human created cell membranes do not exist yet, but that is the next goal, namely, making one. if that goal works, the final goal will be to boot the whole cell to life with the artificial dna inside the artificial cell membrane.

 

keep in mind though - this is simply making life out of non life by copying the structure of a known creature made by nature. this isn't a creature that is designed from the ground up by people, as in a whole new species cooked up by man. but if we can eventually make existing species of bacteria from non-living material, then in the far future we'll probably be able to engineer our own original species from scratch. that's way far in the future though, in my opinion. also, welcome to the boards = )

[iNow]

There is a member here at SFN who is really informed on these topics. He goes by the username "Lucaspa." In several posts, I've seen him reference the following directions.

 

 

 

Call Sigma Chemical Co. at 800-325-3010 and order 1 bottle of catalog number M 7145 and one bottle of R 7131 amino acids solutions (you need both to get all the amino acids http://www.sigmaaldrich.com/sigma/formulation/M5550for.pdf). They will cost you about $40 plus shipping for both. Empty the bottles into a fying pan, turn the heat on low and heat until all the water is evaporated. Then heat for 15-60 minutes. Add water. You will have protocells in the solution.

 

 

And, an overall good link for the laymen to get themselves up to speed on the topic is this:

http://www.theharbinger.org/articles/rel_sci/fox.html

[Mr Skeptic]

Does defrosting a frozen cell count?

[Bobsessed]

Thankyou very much. thats amazing that people actually made DNA, =]

 

And thankyou for welcoming me. I might stick around to get some help with my physics homework.. we're doing momentum.. and I'm very lost!

[iNow]

Thankyou very much. thats amazing that people actually made DNA, =]

 

And thankyou for welcoming me. I might stick around to get some help with my physics homework.. we're doing momentum.. and I'm very lost!

 

I'm not sure if it's accurate for us to say that we've "made DNA," but we are getting quite close, and closer every day... so, stay tuned!

 

 

Momentum, eh? I just remember that if you have two baseballs of equal mass then the one that is travelling faster has more momentum. However, if you have a baseball that weights 1kg and a lead ball that weights 20kg, then the lead ball does not have to travel nearly as fast as the baseball to have the same (or more) momentum.

 

Ugghh... Don't listen to me. There are many cobwebs on that knowledge which was never very solid in the first place. Good luck, and enjoy.

[Mr Skeptic]

Thankyou very much. thats amazing that people actually made DNA, =]

 

And thankyou for welcoming me. I might stick around to get some help with my physics homework.. we're doing momentum.. and I'm very lost!

 

Momentum = Mass X Velocity (compare to Kinetic Energy = 1/2 X Mass X Velocity²)

 

The overall momentum of a system is conserved due to the nature of forces.

[Daecon]

When I saw the thread title I immediately thought of Andrew Crosse.

 

http://en.wikipedia.org/wiki/Andrew_Crosse

[Donut.Hole]

Correct me if I'm wrong, but I thought spontaneous generation (something living out of non-living material) was impossible. Pasteur? proved, for instance, that flies were atrracted to rotting meat and laid eggs on them, creating maggots. He disproved the theory that maggots came directly from rotting meat.

 

It seems really impossible for non-organics to be become organics. How do you get everything to click togehter into life, anyways?

[Cap'n Refsmmat]

Spontaneous generation isn't really relevant. It claimed that organic matter like maggots spontaneously came into existence around decaying (dead) organic matter. We're talking about organic matter coming into existence via its actual necessary ingredients, not via a dead weasel.

[Bobsessed]

I'm not sure if it's accurate for us to say that we've "made DNA," but we are getting quite close, and closer every day... so, stay tuned!

 

 

Momentum, eh? I just remember that if you have two baseballs of equal mass then the one that is travelling faster has more momentum. However, if you have a baseball that weights 1kg and a lead ball that weights 20kg, then the lead ball does not have to travel nearly as fast as the baseball to have the same (or more) momentum.

 

Ugghh... Don't listen to me. There are many cobwebs on that knowledge which was never very solid in the first place. Good luck, and enjoy.

 

thats actually quite helpful.

thankyou.

so, are the people on this site mainly younger or older? like over 20 or under?

you all sound very intelligent.

[Realitycheck]

There are undoubtedly more, but I believe that the leaders in this field are Craig Venter and MIT, both working independently to produce cells from scratch. Venter has developed a synthetic genome that he is trying to transplant into a host cell and MIT has done lots of research into modelling of synthetic cells.

 

http://www.jcvi.org/cms/research/projects/chemical-synthesis-of-the-mycoplasma-genitalium-genome/overview/

 

http://www.mitpressjournals.org/doi/abs/10.1162/106454603322392479

 

I went ahead and bought this article since it looked so interesting. Here is the intro to give you a look at the work that has been done on this subject and where they are driving from.

 

1 Introduction

Like contemporary living cells, under appropriate laboratory conditions future proto-

organisms will sustain themselves chemically, feed from the environment, self-repro-

duce, be capable of evolution, and be able to die under environmental stress. Unlike

actual cells and their proto-cell ancestor, engineered proto-organisms will have an ar-

tificial origin, environment, and metabolism. They will not be made or derived from

existing cells; instead they will be built “from scratch” to operate only in artificial en-

vironments. Although they may have some metabolic pathways common to those in

natural cells, their designed metabolisms may exhibit completely different chemistries.

Proto-organisms have not yet been constructed in the laboratory, partly due to the

physicochemical complexity of assembling such structures and partly because only very

few focused efforts exist worldwide. However, recently several efforts have started.

There are two significantly different approaches to synthesizing primitive life forms:

a bottom-up and a top-down approach. The current contribution is based on a bottom-

up approach concerned with constructing a simple living system from nonliving organic

and inorganic materials through self-assembly, with metabolic processes driven by an

external supply of free energy. The top-down approach concerns itself with systematic

simplification of very simple existing cells.

The presented work on assembling a proto-organism has grown out of a bottom-

up tradition, which has emerged over the past ten years at the intersection between

the origins-of-life studies, nanoscience, new materials, supermolecular chemistry, and

artificial life activities. Our work addresses several of the open questions formulated by

the artificial life community at the 2000 conference in Portland, which can be found in

Bedau et al. [4]. The work mainly addresses question 1, “Generate a molecular proto-

organism in vitro,” but it also touches question 4, “Simulate a unicellular organism over

its entire lifecycle,” and question 5, “Explain how rules and symbols are generated from

physical dynamics in living systems.”

1.1 Bottom Up

Until recently it was difficult to separate the ideas on how to bridge nonliving and

living matter from the theories of the possible origins of life. Experimental bridging

pathways that were believed to be likely have often been proposed as particular origins-

of-life pictures, and these pictures have often been tightly linked to specific molecules

and/or processes. Pictures less dependent on the physicochemical details usually lack

experimental support, but may still be valuable from a theoretical point of view.

The naked-gene approach to bridging nonliving and living matter has for more than

a generation dominated the origins-of-life debate, which from the mid-eighties [12]

through the nineties proposed that the RNA was probably “the first living molecule.”

The RNA world [29, 28] supporters had a very compelling argument: since RNA has

both catalytic and information storage capabilities, it could act simultaneously as DNA

and protein do in contemporary life. Many different polymerization and replication

approaches have been developed [24]. However, to develop a self-replicating RNA

molecule turned out to be a very difficult task [39], and this problem has recently taken

some of the attractiveness from the RNA world picture.

The peptide world, stating that proteins probably were the first biomolecules, per-

haps constitutes the oldest physicochemically based picture of the origins of life [68].

It is based on the fact that proteins can polymerize from amino acids in a prebiotic

environment. The later experiments by Miller and Urey from 1959 [57] demonstrated

laboratory production of amino acids as well as many other key biological compounds

under harsh prebiotic-like conditions. Today we know that most violent or extreme

processes (under high pressure, temperature, or irradiation) that involve simple ele-

ments produce traces of rather complex biomolecules. Examples of such processes

include high explosive blasts [32] and cosmic chemistry in meteorites [16]. One of the

latest and most intriguing experimental developments within the peptide world is the

generation of a self-reproducing peptide system by Ghadiri and coworkers [45, 82].

An alternative origins-of-life picture, the lipid world, was originally developed by

Luisi and coworkers [47] and by Morowitz, Deamer and others in 1988 [60], who have

later worked towards assembling proto-cells based on a self-reproducing lipid vesi-

cle encapsulating a self-replicating RNA proto-gene. Self-reproducing lipid aggregates

(micelles and liposomes, single and bilayer lipid structures) have been developed suc-

cessfully in several laboratories. It is also known that lipids are produced by cosmic

chemistry and probably were readily available at the time of the origins of life. An inter-

esting new twist on the lipid world came recently with the proposed role of atmospheric

aerosols in the origins of life [94]. For example, encapsulating of self-assembling struc-

tures, such as microtubules, within liposomes has also served in attempts to develop

partial proto-cell models [35].

Recently, important players from the RNA world community have joined this en-

capsulation approach, as discussed by Szostack et al. [89]. Their vision consists of a

bottom-up construction, but with rather high-level building blocks. They propose using

an RNA-based chemistry, very similar to the information chemistries in contemporary

natural cells. As they acknowledge, the complexity of the catalysis needed to reproduce

RNA (using an RNA replicase that is still a long way from being able to replicate its own

coding RNA) and the need for metabolic encoding of the building blocks (lipids and

RNA) remain barriers to their approach. In addition, there is no natural physicochemical

integration between the RNA and the lipid container.

Another proto-cell vision has been developed by Pohorille and Deamer [70]. The

starting point for their proposal is also the self-assembling dynamics of lipids to form

lipid bilayer vesicles (liposomes); however, they suggest encapsulating modern cell or-

ganelles. They discuss different versions of artificial cells for different biotechnological

purposes, with variations on RNA- and DNA-based information chemistries, as well

as metabolisms, noting, as do Szostak et al. [89], that there are significant technical

hurdles to making these complex chemistries work even when using existing cellular

organelles. They conclude:

Many individual components needed for such structures have already been

developed and many others are likely to be constructed in the near future. The

main challenge now is to encapsulate them in a single cellular compartment and

ensure that they will work in concert in a controlled manner.

This critique to some extent applies to all bottom-up approaches.

The bottom-up approach also has attracted many theoretical and computational con-

tributions. The notion of a hypercycle is a powerful theoretical concept proposed

by Eigen in 1971 [20]. The hypercycle is a cooperative structure of self-replicating

proto-genes. Also in 1971, Ganti [27] proposed a cooperative structure coupling a

container, a metabolism, and a genetic system, which at least at a conceptual level

is quite similar to our proposed proto-organism. This notion of cooperative struc-

tures being a key element for the bootstrapping of chemical systems to becoming

biological systems has been the most important driver for the theory-driven origin-

of-life approaches. Such approaches span rather realistic model systems with auto-

catalytic sets of polymers as developed by Farmer et al. in 1986 [23], Kauffman in

1986 [42], and Bagley and Farmer in 1991 [3]. Lately, an interesting new idea has

emerged based on autocatalytic lipid structures, due to Segre et al. [83]. Wachter-

hauser [98] has proposed mineral-surface-based metabolic processes as the key boot-

strap for the first self-reproducing lipid systems. Random graph generalizations of

the cooperative feedback concept for proto-genetic systems were developed by Ras-

mussen in 1985 [75] and 1988 [76], and spatial hypercycle generalizations were devel-

oped by Hogeweg and coworkers [6]. Study of spatially extended systems showed

that the hypercycle organization persists in the face of parasites in such settings, due

to the formation of spiral waves. As a major simplification it was shown by Mc-

Caskill and coworkers [54, 55] that hypercycles, or other reaction based cyclic cooper-

ative feedback structures, are not necessary for the stabilization of distributed catalysis

when one uses proximity in space. Recently, abstract self-reproducing computational

proto-cells have been developed by Ikegemi and coworkers [67]. These proto-cells

have more realistic physical properties encoded than (for example) the intriguing self-

reproducing loops proposed by Langton in 1984 [44] and by Sayama in 1998 [84], and

for that reason they are more informative for the construction of physicochemical proto-

cells.

In addition to the notion of cooperative structures in chemical networks, two other

theoretical and computational traditions are important for our proto-organism work:

(a) the detailed molecular dynamics (MD) simulation approach [100, 51] together with

(b) the traditional lattice gas [7], lattice Boltzmann [41], and Ginzburg-Landau [38] ap-

proaches. Adding a technique for intermediate time- and length-scale simulation, the

MD lattice gas [52, 66], we have the necessary components for a developing a pre-

dictive, 3D, virtual proto-organism simulation. Rajagopalan [74] has compiled a nice

review of self-assembly simulations, but a comprehensive multiscale simulation is not

yet available.

Our proto-organism design is inspired both by the above theoretical and computa-

tional ideas and by the experimental concepts for a proto-cell due to Luisi and cowork-

ers [49], but our model also differs from this and other proposals in several aspects:

1. Our focal point is a minimalistic, thermodynamic coupling between the three

functional structures: container, metabolism, and genes. We do not start with a

self-replicating container or a self-replicating gene, which is then combined.

2. Instead of RNA, we envision simpler molecules, such as peptide nucleic acids

(PNAs) [64, 63]. Due to their hydrophobic backbone, these may be easier to couple

with the lipid layer than RNA, and they are also easier to synthesize.

3. Instead of sophisticated ribozymes, we consider very simple short oligos that are

capable of enzymeless self-replication by means of a ligation mechanism [96, 97].

4. As in the other proto-cell proposals, we utilize the lipid to keep the cooperative

structure together, although the proto-genetic activity is not on the inside of a

vesicle [1] but on the outside of a lipid aggregate. We can therefore work with

simpler lipid structures such as micelles.

5. We make extensive use of the differences between the thermodynamic properties

of the lipid phase and those of the water and the lipid-water interface, and as a

result we obtain a quite different chemistry.

1.2 Top Down

The top-down approach starts with contemporary cells with very small genomes. Exper-

iments with a simple bacterium, Mycoplasma genetalium [26, 36] indicate that cells can

have much of their genome removed and remain alive. Current estimates of the minimal

genome size based on this approach are ≈300–350 genes. The minimal genome size

obtained from these experiments may be considered an upper bound on the genome

size expected for simple proto-cells based on translated protein chemistry. Readjust-

ment to deletions via retro-evolution of the cells and complementation has not been

fully investigated. These minimal cells may still have artefacts in their genome that are

needed to support physical and metabolic structures that have been required along the

evolutionary path of the original bacteria, but that may not be needed for proto-cells.

Recently Venter and Smith [30] have received financial support from the U.S. govern-

ment (DOE) to create new, more primitive life forms using this top-down approach.

In parallel with this experimental top-down approach, a push for whole-cell simu-

lations is under way within the systems biology community; see for example Science,

299 (2002). These efforts are driven by a growing understanding of the details of the

metabolic pathways and genetic networks. This tradition is concerned with representa-

tion and simulation of life as it is, as opposed to the artificial life community’s focus on

a synthesis and simulation of life as it could be. It is worth noting, however, that these

whole-cell simulations could in a natural manner test and benchmark their approaches

by simulating the much simpler proto-cells currently under development—including

the proposed proto-organism in this article.

[antimatter]

I never quite realized the extent of the phrase "It's difficult to read articles on the computer"...

[thedarkshade]

has anybody ever made a cell out of non-living matter?

Well Miller's experiment did produce organic substances

and can you make DNA?

Well, as nature managed to do it, mankind some time probably will.

 

There is a member here at SFN who is really informed on these topics. He goes by the username "Lucaspa."

He rocks, definitely!

 

I never quite realized the extent of the phrase "It's difficult to read articles on the computer"...

It's hard, I agree!

[lucaspa]

It may be silly, but I'm fascinated by the idea of creating something living out of non-living things.

has anybody ever made a cell out of non-living matter?

and can you make DNA?

 

Yes to the first, no to the second.

 

Start here for getting a cell starting with amino acids:

http://www.theharbinger.org/articles/rel_sci/fox.html

http://www.siu.edu/~protocell/

 

Neither DNA nor RNA will readily form from abiotic reactions. However, there are nucleic acids that will do so:

20. L Orgel, A simpler nucleic acid. Science 290: 1306-1307, Nov 17, 2000. 222/sciencemag.org/cgi/content/full/290/5495/1306 Threose nucleic acids are easy to synthesize under prebiotic conditions and act like RNA chemically.