Minimum Complexity of Life on Earth

Minimum Complexity of Life on Earth

http://www.evidenceunseen.com/articles/science-and-scripture/the-origin-of-life/

Pelagibacter ubique
Bacteria
1,354

Pelagibacter ubique




Scientific classification (Candidatus)
Domain: Bacteria
Phylum: Proteobacteria
Class: Alphaproteobacteria
Subclass: Rickettsidae
Order: Pelagibacterales
Family: "Pelagibacteraceae"
Genus: Pelagibacter
Species: P. ubique
Binomial name
Candidatus Pelagibacter ubique
Rappé et al. 2002

Pelagibacter, with the single species P. ubique, was isolated in 2002 and given a specific name,[1] although it has not yet been validly published according to the bacteriological code.[2] It is an abundant member of the SAR11 clade in the phylum Alphaproteobacteria. SAR11 members are highly dominant organisms found in both salt and fresh water worldwide — possibly the most numerous bacterium in the world, and were originally known only from their rRNA genes, which were first identified in environmental samples from the Sargasso Sea in 1990 by Stephen Giovannoni's laboratory in the Department of Microbiology at Oregon State University and later found in oceans worldwide.[3] P. ubique and its relatives may be the most abundant organisms in the ocean, and quite possibly the most abundant bacteria in the entire world. It can make up about 25% of all microbial plankton cells, and in the summer they may account for approximately half the cells present in temperate ocean surface water. The total abundance of P. ubique and relatives is estimated to be about 2 × 1028 microbes.

The genome of P. ubique strain HTCC1062 was completely sequenced in 2005 showing that P. ubique has the smallest genome (1,308,759 bp) of any free living organism[5] encoding only 1,354 open reading frames (1,389 genes total)

it still has metabolic pathways for all 20 amino acids and most co-factors.





Thermoplasma acidophilum
Archaea
1,509
Aquifex aeolicus
Bacteria
1,512
Picrophilus torridus
Archaea
1,535
Helicobacter pylori
Bacteria
1,591
Methanopyrus kandleri AV19
Archaea
1,692
Methanococcus jannaschii
Archaea
1,738
Streptococcus pyogenes
Bacteria
1,752
Methanobacterium thermoautotrophicum
Archaea
1,855
Thermotoga maritima
Bacteria
1,877
Thiomicrospira crunogena XCL-2
Archaea
1,922

One Way To Think About the Complexity of the “Simplest” Life Form

http://blog.drwile.com/?p=8161

bacterium Mycoplasma genitalium. It’s genome has 582,970 base pairs and 525 genes.3 While it is a parasite, it performs all the standard functions of life on its own. It just uses other organisms (people as well as animals of the order Primates) for food and housing. Thus, while it cannot exist without other organisms, it might be the best indicator of how “simple” life can get. a scientist from Venter’s lab teamed up with several scientists from Stanford University to produce a computer simulation of the bacterium!

Their work, which seems truly marvelous, gives us deep insight into how complex the “simplest” living organism really is.

Now let’s look at this in very practical terms. In order to be able to match the speed at which the organism operates, this less-than-complete simulation required a cluster of 128 computers to get the job done. Think about that for a moment. In order to simulate most (but not all) of the processes that take place in an analog for what might be the simplest possible living organism, the authors needed the power of 128 computers running together! That should tell us something very clearly:

There is no such thing as a simple living organism.
The more we understand life, the more clear it becomes that even the “simplest” version of it has to be the result of design.

I have always been fascinated by the question, “How simple can life get?” After all, anything that is alive has to perform certain functions such as reacting to external stimuli, taking in energy and converting that energy to its own use, reproducing, etc. Exactly how simple can a living system be if it has to perform such tasks? Many biologists have investigated this question, but there isn’t a firm answer. Typically, biologists talk about how simple a genome can be. The simplest genome belongs to a bacterium known as Carsonella ruddii. It has 159,662 base pairs in its genome, which is thought to contain 182 genes.1 However, it is not considered a real living organism, as it cannot perform all the functions of life without the help of cells found in jumping plant lice.


The bacterium known as Pelagibacter ubique has the smallest genome of any truly free-living organism. It weighs in at 1,308,759 base pairs and 1,354 genes.2 However, there is something in between these two bacteria that might qualify as a real living organism. It is the bacterium Mycoplasma genitalium. It’s genome has 582,970 base pairs and 525 genes.3 While it is a parasite, it performs all the standard functions of life on its own. It just uses other organisms (people as well as animals of the order Primates) for food and housing. Thus, while it cannot exist without other organisms, it might be the best indicator of how “simple” life can get.

If you follow science news at all, you might recognize the name. Two years ago, Dr Craig Venter and his team constructed their own version of that bacterium with the help of living versions of the bacterium, yeast cells, and bacteria of another species from the same genus. Well, now a scientist from Venter’s lab teamed up with several scientists from Stanford University to produce a computer simulation of the bacterium!

Their work, which seems truly marvelous, gives us deep insight into how complex the “simplest” living organism really is.


Let’s start with what the computer simulation actually accomplished. It modeled all the inputs and outputs of the bacterium’s 525 genes throughout a single cell cycle. In other words, it simulated how the genome produces proteins, how those proteins interact with other proteins, and how the entire system is regulated. It followed these processes through all the events leading up to and including the cell reproducing itself.4

Now that’s a lot of work! How did the authors do it? Well, they looked at over 900 different scientific papers that had been produced on the inner workings of Mycoplasma genitalium, and they identified 1,900 specific parameters that seem to govern how the cell operates. There were several discrepancies that were found among the papers involved, and as a result, there was a lot of reconciliation that had to be done. The details of this reconciliation and other matters are found in a 120-page supplement to the 12-page scientific paper.

Once the reconciliation of these studies was accomplished, the essential workings of the cell were split into 28 separate modules that each governed specific functions of the cell. For example, one module dealt with metabolism, while another dealt with the activation of proteins once they were produced. Once each module was built and tested individually, the modules were then joined by looking at what they produced every second. If the products of one module were the kinds of chemicals used by a second module, those products were then treated as inputs to the second module for the next second of computation. The computation proceeded like this (checking the inputs and outputs of each module) for about 10 hours, which is roughly the time it takes a real Mycoplasma genitalium to reproduce.

Why would a group want to undertake such a complex endeavor? Well, one obvious reason is the reconciliation that I mentioned previously. As independent papers, each of the 900 studies to which the authors referred made sense. However, when the authors started using the results of those studies in a model that tries to take all the molecular processes of a cell into account, they found that some results didn’t mesh well with others. The reconciliation that had to take place to get the simulation working will help us better understand the limits of many of the studies related to Mycoplasma genitalium and hopefully will lead to more detailed studies that will slowly wipe away such discrepancies. Also, as the authors state, these kinds of models will:

…accelerate biological discovery and bioengineering by facilitating experimental design and interpretation. Morever, [this study and others] raise the exciting possibility of using whole-cell models to enable computer-aided rational design of novel microorganisms.

So in the end, not only will such models help us better design and interpret experiments, they might one day lead us to ways that we can engineer new microorganisms.

This is fantastic work, and I do think it opens up new vistas in cell and molecular biology. However, we need to pull back for a moment and think about the direct implications of this computer simulation. It simulated, in very basic terms, the molecular interactions that occur in a cell that might be a good analog for the simplest possible life form. It skipped over a lot of details, of course, so it is not a complete simulation by any means. Nevertheless, it is a great first step towards understanding how a living system really works.

Now let’s look at this in very practical terms. In order to be able to match the speed at which the organism operates, this less-than-complete simulation required a cluster of 128 computers to get the job done. Think about that for a moment. In order to simulate most (but not all) of the processes that take place in an analog for what might be the simplest possible living organism, the authors needed the power of 128 computers running together! That should tell us something very clearly:

There is no such thing as a simple living organism.
The more we understand life, the more clear it becomes that even the “simplest” version of it has to be the result of design.

http://www.sciencedirect.com/science/article/pii/S0092867400812635

There is still a gap between descriptions of prebiotic events and the last common ancestor. Intermediate stages must have involved simpler organisms with much smaller genomes. The question is whether it is possible to infer some of their major characteristics. It has long been recognized that most genetic information is not essential for cell growth and division. Statistical analysis of ∼80 randomly selected chromosomal loci for Bacillus subtilis has led to the suggestion that the minimum cellular genome size is of the order of 562 kb (Itaya 1995).

This figure is comparable with the size of the Mycoplasma genitalium genome, which is 580 kb long and codes for 482 genes (Fraser et al. 1995).

It is unlikely that such a large array of sequences involved in replication, transcription, and translation were already present in the first DNA/protein organisms.

Most enzymes are recognized to have arisen by gene duplication. The uncertainty is the number of enzymes that did not arise in this manner, i.e., the starter types. In some cases, the starter types may stem from slow nonenzymatic reactions where the protein improves on a previously sluggish process, e.g., pyridoxal catalyzed transaminations.

All known life forms share a common pool of highly conserved genetic information

One Way To Think About the Complexity of the “Simplest” Life Form

http://blog.drwile.com/?p=8161

bacterium Mycoplasma genitalium. It’s genome has 582,970 base pairs and 525 genes.3 While it is a parasite, it performs all the standard functions of life on its own. It just uses other organisms (people as well as animals of the order Primates) for food and housing. Thus, while it cannot exist without other organisms, it might be the best indicator of how “simple” life can get. a scientist from Venter’s lab teamed up with several scientists from Stanford University to produce a computer simulation of the bacterium!

Their work, which seems truly marvelous, gives us deep insight into how complex the “simplest” living organism really is.

Now let’s look at this in very practical terms. In order to be able to match the speed at which the organism operates, this less-than-complete simulation required a cluster of 128 computers to get the job done. Think about that for a moment. In order to simulate most (but not all) of the processes that take place in an analog for what might be the simplest possible living organism, the authors needed the power of 128 computers running together! That should tell us something very clearly:

There is no such thing as a simple living organism.
The more we understand life, the more clear it becomes that even the “simplest” version of it has to be the result of design.

The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time

http://www.sciencedirect.com/science/article/pii/S0092867400812635

There is still a gap between descriptions of prebiotic events and the last common ancestor. Intermediate stages must have involved simpler organisms with much smaller genomes. The question is whether it is possible to infer some of their major characteristics. It has long been recognized that most genetic information is not essential for cell growth and division. Statistical analysis of ∼80 randomly selected chromosomal loci for Bacillus subtilis has led to the suggestion that the minimum cellular genome size is of the order of 562 kb (Itaya 1995).

This figure is comparable with the size of the Mycoplasma genitalium genome, which is 580 kb long and codes for 482 genes (Fraser et al. 1995).

It is unlikely that such a large array of sequences involved in replication, transcription, and translation were already present in the first DNA/protein organisms.

From the book Alberts, Molecular biology of the cell:

Heredity is perhaps the central feature of life. Not only must a cell use raw materials to create a network of catalyzed reactions, it must do so according to an elaborate set of instructions encoded in the hereditary information. The replication of this information ensures that the complex metabolism of cells can accurately reproduce itself.

This information could not have arisen through mutation and natural selection, as there was no replicating cell yet....... so the only mechanism that remains is chance, physical necessity, or a mix of both. In the same way , as it is unlikely , that Hamlets Shakespeare arises by chance, so much less the information that must be encoded in DNA to make the first living cell. Thats by its own pretty much a check mate for naturalism.....

http://phys.org/news/2013-09-assumptions-life.html#jCp

But for the hypothesis to be correct, ancient RNA catalysts would have had to copy multiple sets of RNA blueprints nearly as accurately as do modern-day enzymes. That's a hard sell; scientists calculate that it would take much longer than the age of the universe for randomly generated RNA molecules to evolve sufficiently to achieve the modern level of sophistication. Given Earth's age of 4.5 billion years, living systems run entirely by RNA could not have reproduced and evolved either fast or accurately enough to give rise to the vast biological complexity on Earth today.


The RNA world hypothesis: the worst theory of the early evolution of life

http://www.ncbi.nlm.nih.gov/pubmed/22793875

(i) RNA is too complex a molecule to have arisen prebiotically;
(ii) RNA is inherently unstable;
(iii) catalysis is a relatively rare property of long RNA sequences only; and
(iv) the catalytic repertoire of RNA is too limited.