Preadaptations

[Phronesis]

Not me, why? You get those for being rude and disruptive, or so I am told.

Mmm, true .

 

[alloytoo]

Not me, why? You get those for being rude and disruptive, or so I am told.

Swearing and obscenities (I don't believe in Blasphemy) apparently

 

[Phronesis]

First Discovery Of 'Animals-only' Pigment Bilirubin In Plants

ScienceDaily (Mar. 23, 2009) — In a first-of-its-kind discovery that overturns conventional wisdom, scientists in Florida are reporting that certain plants — including the exotic "White Bird of Paradise Tree" — make bilirubin. Until now, scientists thought that pigment existed only in animals. The finding may change scientific understanding of how the ability to make bilirubin evolved, researchers say.

In the new study, Cary Pirone and colleagues note that bilirubin is a brownish yellow substance resulting from the liver's breakdown of hemoglobin, the red pigment that carries oxygen in the blood. Parents know bilirubin as the stuff that discolors the skin of newborns with neonatal jaundice, sometimes requiring phototherapy, treatment with light. Bilirubin also gives a yellowish tinge to the skin of patients with jaundice resulting from liver disease. Until now, scientists never dreamed that plants, as well as animals, produce bilirubin.

The researchers used two powerful laboratory techniques, liquid chromatography and nuclear magnetic resonance, to detect bilirubin in fruit of the white bird of paradise tree. The fruits contain unusual, orange-colored, furry seeds, and bilirubin turns out to be the coloring agent. They also found the pigment in two closely related plant species. The discovery may stir evolutionary research to understand why and how plants make what everyone regarded as an animals-only pigment, they suggest.

More here:
Animals’ jaundice pigment found in plants

The pigment bilirubin, long known as a leftover in the breakdown of animal blood, has turned up in the blood-free world of plants.

In people and many other animals, bilirubin puts the yellow into bruises and into the complexion of jaundice sufferers.

Now it turns out that bilirubin also puts the screaming orange into the fuzz on seeds of the white bird of paradise tree, says Cary L. Pirone of Florida International University in Miami. A sister species with orange and blue flowers also carries bilirubin, Pirone and her colleagues report online February 10 in the Journal of the American Chemical Society.

“It’s the first time bilirubin has been found in the plant kingdom,” Pirone says.

This flashy pigment has been hiding in plain sight in tropical gardens virtually worldwide.

“The birds of paradises are not rare plants,” says botanist John Kress of the Smithsonian National Museum of Natural History in Washington, D.C. “But here is a wonderful new discovery.”

Black, pea-sized seeds of the white bird of paradise tree (Strelitzia nicolai) grow an aril, or tuft of waxy ribbons covering each seed base. The aril, as Pirone puts it, looks “shockingly orange.”

Intense color may help catch the eye of passing birds, known to eat the plant’s seeds and thus give the seeds a lift to new territory. Unlike many other plant colors, this orange doesn’t fade easily, says coauthor David Lee, also of Florida International. He has found arils of seed specimens still glowing after decades in an herbarium.

Pirone began studying the orange pigment serendipitously. Examining arils in the bird of paradise family, she found that the orange compound didn’t match the chemical properties of any known plant pigments. The light wavelengths the pigment absorbed didn’t fit the patterns for carotenoids, for example, but the way it reacted with polar versus nonpolar solvents didn’t make sense for other pigment classes.

When Pirone worked out the mass of the pigment molecules, bilirubin emerged as one of the possible suspects. To pin down the pigment’s identity, she needed to run a more detailed test, exposing the pigment to a magnetic field. That required at least a milligram of the pure compound, but the purification method she had used for tiny quantities failed when she tried to scale it up. In the end, she repeated the small-scale procedure some two dozen times to get a quantity she could use.

The nuclear magnetic resonance tests confirmed that Pirone had bilirubin.

The bilirubin in plants doesn’t come from breaking down hemoglobin, the compound that gives blood its red hue. But pigments in hemoglobin and plants’ light-trapping chlorophyll molecules have similar ring structures, says plant biochemist Dean DellaPenna of Michigan State University in East Lansing. Breaking down chlorophyll can yield bilirubin too.

Plants maintain tight control over their powerful chlorophyll molecules — “harvesting light and splitting water is risky business,” DellaPenna says. Biochemists are still working out the steps for chlorophyll breakdown.

Researchers have found that plant enzymes open the chlorophyll molecule to form a substance that could turn into bilirubin with just one more step. In looking at the new paper, DellaPenna says, “The most interesting thing is that this suggests the first couple of steps of degradation are identical in plants and animals.”

 

[rwenzori]

Ah! Billy Rubin! Hannibal Lecter's clever deceit in Silence of the Lambs!


Yes - "bilirubin, a pigment found in faeces and the colour of Dr. Chilton's hair" LOL!

 

[Phronesis]

Cough, cough, look at you, "always" pointing out the beauty and awe in nature...

 

[rwenzori]

Cough, cough, look at you, "always" pointing out the beauty and awe in nature...

Ever read The Silence of the Lambs?

 

[Phronesis]

Ever read The Silence of the Lambs?

Did the book move you, resulting in a preadaptation that causes you to point the beauty and awe in nature?

Back to preadaptations:
Evolution Of Fins And Limbs Linked With That Of Gills

ScienceDaily (Mar. 25, 2009) — The genetic toolkit that animals use to build fins and limbs is the same genetic toolkit that controls the development of part of the gill skeleton in sharks, according to a new study.

And the toolkit (Retinoic acid receptors etc.) emerged way before body plans were on the cards.

 

[rwenzori]

Did the book move you, resulting in a preadaptation that causes you to point the beauty and awe in nature?

Clearly you have not read it. You really should read a bit more widely you know.

 

[Phronesis]

Oops, it should have read:
Did the book move you, resulting in a preadaptation that causes you to point the "beauty" and "awe" in nature?

 

[rwenzori]

Oops, it should have read:
Did the book move you, resulting in a preadaptation that causes you to point the "beauty" and "awe" in nature?

A census taker once tried to test me. I ate his liver with some fava beans and a nice chianti - H. Lecter.

 

[Phronesis]

Interesting creature:
Micromonas

Gave rise to plants (See figure)

Just look at its genes:
Genes from tiny marine algae suggest unsuspected avenues for new research

By sequencing the DNA of two tiny marine algae, a team of scientists has opened up a myriad of possibilities for new research in algal physiology, plant biology, and marine ecology. The project was led by Alexandra Worden at the Monterey Bay Aquarium Research Institute (MBARI) and the Joint Genome Institute (JGI). The genome analyses involved a collaborative effort between MBARI, JGI, and an international consortium of scientists from multiple institutions, including University of Washington, Ghent University (Belgium), and Washington University in St. Louis. Initial discoveries from the research appear in the April 10, 2009 edition of Science magazine.

Biologists generally agree that all land plants, from tiny mosses to giant redwoods, evolved from an ancestral green alga. Some of the closest representatives of these ancestral green algae living today are thought to be the Prasinophytes, a group of microscopic green algae found across the world's oceans.

Microbial oceanographer Alexandra Worden led a team of scientists that sequenced the genomes of two Prasinophytes in the genus Micromonas. Each Micromonas cell is only about one fiftieth the width of a human hair. However, they are widespread and may serve as important links in marine food webs. They may also influence the amount of carbon dioxide the oceans take up from the atmosphere.

Worden's team spent four years compiling a complete list of the approximately 21 million chemical building blocks (called bases) that make up Micromonas' DNA. The recent Science paper highlights key aspects of this genetic "Morse code." The paper also compares Micromonas' genes with genes found in other organisms.

A microscopic alga with leaves?

Worden and her fellow researchers discovered that Micromonas carries a significant number of genes that are not found in the genomes of other green algae (at least not in the five or six other species sequenced to date). Some of these genes, however, are found in land plants or bacteria. Worden's team is currently trying to find out the functions of these genes in Micromonas. Such information will help researchers better understand how Micromonas interacts with its environment and with other marine organisms.

According to Worden, "One of our main findings is that some genes that were thought to be land-plant specific were also found in Micromonas. It's possible that land plants could have developed these genes and Micromonas also developed them. Or perhaps an organism (the ancestral alga) that preceded both land plants and Micromonas had them, which is the simpler explanation."

For example, the researchers found evidence that Micromonas has genes that scientists previously temporally associated with the development of leafy plants. Obviously, Micromonas never developed leaves. Thus Worden's research suggests that such genes may have other functions that are not yet understood.

Another unexpected finding was that Micromonas contains genes associated with sexual reproduction (as opposed to simply dividing into two cells asexually). As Worden says, "Formerly it was thought that these algae do not have sex. Now it really looks as though they do have sex. No one has seen it, but this could be because laboratory conditions are not correct for switching to this form of reproduction."

Simply knowing Micromonas can reproduce sexually could lead to additional discoveries. Worden explains, "Now that we have the sequences for those genes [for sexual reproduction], we could look for them being expressed in the field. Then we could try to figure out the conditions triggering sexual reproduction and the ecological avenues it opens for Micromonas. In addition, if we could get Micromonas to reproduce sexually in the lab, we might be able to develop a system for permanently "knocking out" genes [deactivating or removing them from an organism's DNA] and advance our knowledge of their functional roles. We don't have such a system yet for any of the more widespread marine algae."

Filling in the unknowns

In addition to highlighting a number of genes whose functions are known from other organisms, Worden's team found that a large number of the genes in Micromonas have no known function. She explains, "We know they're real—they're expressed and we've seen them in other organisms—but they're not genes that anyone has characterized, so no one knows what they do."

Worden continues, "As an ecologist starting out on this project, I was trying to find out what genes were ‘special’ to each genome, or those shared by the two Micromonas strains but not other competitors. By looking at the function of such genes we could then learn more about the different niches of these organisms... It turns out that we don’t yet know the function of many of these genes—but we know we need to target them. This highlights the grand challenge ahead. With a focused effort on cell biology, we will be able to discover the function of such genes. This will advance our understanding of these organisms and their ecology as well as metagenomic analyses. It's really basic cell biology, but the implications for doing ecological work are huge."

Figuring out what these genes "do" could also help researchers in other fields, such as plant science. As Worden put it, "A lot of important agricultural plants are already sequenced. But there's a big difference between having the sequence and making meaning of the sequence. For example, there is a huge list of genes that contain 'domains of unknown function.' We've seen these domains in many organisms and we know they must be real, but we don't know their cellular function. If we can fill in such blanks, using these ‘simpler’ organisms, we'd be doing everyone a favor."

Finally, the research will help researchers understand how algae respond to changes in their environment. This should give scientists a better idea of how marine algae take up carbon dioxide from the atmosphere, a central feature of the roles they play in mitigating greenhouse warming of the Earth. As Worden points out, "There is a lot of work that needs to be done integrating our discoveries with research being done on other marine microbes in order to understand more about community interaction, synergies, and how together they shape ecosystem responses. With this in mind we can develop a more mechanistic understanding of how carbon is moving within the marine environment and develop more sensitive tools for investigating carbon flow."

Sequencing the genomes of two small marine algae may not seem to have many real-life benefits. But when you consider that these organisms share genes with other microbes and suites of genes with land plants, the possibilities are virtually endless. Worden and her team are looking forward to further exploration of the "toolbox" of genes used by the multitude of organisms that keep our planet green.

Fascinating . Genes for the development of leaves and sexual reproduction. And the most parsimonious explanation is that the emergence of these genes preceded both land plants and Micromonas. The trend continues.... genetic tool kits for multicellularity and before the emergence of multicellularity, genes for eyes, a nervous system, bones, body shape etc. before the emergence of them. And on and on and on and on....

Can anyone say FLE ?

 

[rwenzori]

Can anyone say FLE ?

Not I, said the fly.

 

[Phronesis]

Not I, said the fly.

Wow, another insightful comment by MyBB's "upstanding" and "exemplary" atheist materialist. You set a good example lol.

But, just to interrupt you for a second there away from your "insightful" thoughts (my apologies lol), have a look at this:

Key Protein In Cellular Respiration Discovered

ScienceDaily (Apr. 14, 2009) — Many diseases derive from problems with cellular respiration, the process through which cells extract energy from nutrients. Researchers at Karolinska Institutet in Sweden have now discovered a new function for a protein in the mitochondrion - popularly called the cell's power station - that plays a key part in cell respiration.

Just to give a little background on mitochondria and what they do and how they got into cells,

1) Mitochondrial oxidative phosphorylation produces the majority of cellular ATP through the electron transport chain (ETC) under aerobic conditions in eukaryotic cells.
2) The principal oxidative phosphorylation components of the ETC consists of four major multi-subunit complexes including
A) NADH Coenzyme Q reductase (complex I)
B) Succinate Coenzyme Q reductase (complex II)
C) Ubiquinol cytochrome c reductase (complex III)
D) Cytochrome c oxidase (CcO, complex IV).
3) The fifth component involved in oxidative phosphorylation and responsible for ATP synthesis is F0F1 ATP synthase (complex V) (This baby)

4) Just to give a brief idea of the mechanism involved:
According to the chemiosmotic theory, electrons pass through the ETC (complex I-IV) resulting in the transportation of protons (H+) from the mitochondrial matrix into the intermembrane space (IS). This results in an electrochemical gradient known as the mitochondrial membrane potential (∆Ψm = negative 150-180mV in matrix) and a proton gradient (∆pH). Together, the ∆Ψm and ∆pH results on the formation of the proton motive force (PMF or ∆p = (∆Ψm - 60∆pH). The PMF in turn is used to drive the synthesis of adenosine triphosphate (ATP) from adenosine diphosphate (ADP) at complex V.

The PMF is generated by the ETC (complex I-IV). Complex I catalyzes the oxidation of reduced nicotinamide adenine dinucleotide (NADH) to oxidized nicotinamide adenine dinucleotide (NAD+), thereby transferring electrons to Coenzyme Q (Ubiquinone, CoQ), resulting in the formation of dihydroubiquinone (CoQH2, reduced CoQ). CoQ a lipid soluble electron carrier situated in the lipid bilayer of the inner mitochondrial membrane.


So why is this important and how does it relate to the article above?
Well, first of all, it is believed that mitochondria existed as bacteria that fused with ur-eukaryotic cells to form mitochondria.




Now for the interesting part: From the article:

Every time we take a breath, our blood transports oxygen to the mitochondria, where it is used to convert the nutrients in our food to a form of energy that the body can use. Problems with this process, which is called cellular respiration, have been linked to a number of morbid conditions, from unusual genetic diseases to diabetes, cancer and Parkinson's, as well as to the normal ageing process. Despite the fact that cellular respiration is so basic, there is much scientists have yet to understand about how it is regulated.

Cellular respiration depends on proteins synthesised outside the mitochondrion and imported into it, and on proteins synthesised inside the mitochondrion from its own DNA. Researchers at Karolinska Institutet have now shown that a specific gene (Tfb1m) in the cell's nucleus codes for a protein (TFB1M) that is essential to mitochondrial protein synthesis. If TFB1M is missing, mitochondria are unable to produce any proteins at all and cellular respiration cannot take place.

"Mice completely lacking in TFB1M die early in the foetal stage as they are unable to develop cellular respiration," says Medodi Metodiev, one of the researchers involved in the study, which is presented in Cell Metabolism. "Mice without TFB1M in the heart suffer from progressive heart failure and increase mitochondrial mass, which is similar to what we find in patients with mitochondrial diseases."

The scientists believe that the study represents a breakthrough in the understanding of how mitochondrial protein synthesis is regulated, and thus increases the chances of one day finding a treatment for mitochondrial disease, something which is currently unavailable.

Look at the gene TFB1M

The transcription of genes from mitochondrial DNA requires a mitochondrial RNA polymerase (see POLRMT, MIM 601778) and a DNA-binding transcription factor (see TFAM, MIM 600438). Transcription factor B1 (TFB1M) is a part of this transcription complex.

The mitochondrion has its own genome, however for it to function, it relies totally on a gene that is not present in its genome (the gene is encoded in the nucleus of eukaryotes). What is even better is that this gene is dispersed across all phyla.

So, another interesting preadaptation. This time a transcription factor needed to activate mitochondria long before they even existed. Sort of like the gene was just waiting for mitochondria to come onto the scene and unlock their energy producing capabilities for cells.

 

[rwenzori]

I see I am being censored again. Did you bleat to the mods TelePhrone?

 

[Phronesis]

Old genes with new tricks...
Old Genes Can Learn New Tricks, Horned Beetles Show

ScienceDaily (May 13, 2009) — A popular view among evolutionary biologists that fundamental genes do not acquire new functions has been challenged by a new study in the Proceedings of the National Academy of Sciences.

 

[Phronesis]

The trend continues: Sensory perception: Eyes were on the cards... anyway.

Molecular Complex Essential For Vision Identified In Fungi

ScienceDaily (June 2, 2009) — An international team of researchers has identified one of the protein components of a molecular complex that allows light reception in a laboratory fungus.

Look when fungi emerged:

Way before eyes emerged, yet a complex that is essential for vision was present. Fungi and multicellularity also emerged at around the same time, yet toolkits for multicellularity were also present way before it emerged. All that was needed was a little atmospheric oxygen to unlock the pathways towards multicellular body plans (>3 cell types). What is even more interesting is that the increase in atmospheric oxygen is due to the presence of life itself....

It gets more interesting with regards to the madA and madB genes in fungi. Domains of these genes are present in bacteria as well as in archaea, both organisms that emerged before fungi.

The structure of the related photoreceptor (E-value = 6.9E-36) from Neurospora

 

[Phronesis]

Which process would you use in order to make sure a certain species emerges out of random processes and optimize them for a specific niche as well?
Which mechanism would you implement?
How would you constrain a process towards certain outcomes by taking randomness into account?

1) Evolution is probably your best bet.
2) An optimal code, perhaps 3? Highly optimal machinery?
3) Well, you won't need to constrain the process, as it is inevitable that certain outcomes will be reached... as planned.

So what does science tell us about our existence.

1) Common descent with modification (evolution) is an explanation for the genetic diversity we observe.
2) Mechanisms and "software" for the diversity is explained by:
A) A superbly optimal genetic code.
An epigentic code we are only starting to understand.
And a ribosomal code. Another code sure to reveal more secrets.
B) Biomolecular machines outstripping our best attempts at nano-machinery. Of course these are governed by the 3 codes.
C) What is the nature of evolution? Highly constrained and biased.

Question Of Chance In Evolution Addressed​

What is remarkable is that the molecular genealogy of the living species shows their origin only 15 million years ago, with the same trajectory as in the distant past! Evidence suggests that trajectory has occurred again and again in other groups. The authors argue that the original trajectory was highly contingent on a set of initial conditions, but that given the possibilities afforded by time, a genetic background would arise (like flipping a coin long enough to achieve 10 heads or tails in a row) that was visible to natural selection, most likely driven by predation. Acting together, the eventual realization of a particular genetic and developmental channel, and natural selection opened the way for an adaptive solution.

Replay the tape of life and similar outcomes should be inevitable. Now compare these results to some of our own designed evolutionary software...
Memetic algorhitms:
Memetic Algorithms (MAs) are search techniques used to solve problems by mimicking molecular processes of evolution including selection, recombination, mutation and inheritance. In order to understand the basics, a few important aspects of MAs need to be considered (Figure 1).

• The fitness landscape needs to be finite.
• The search space of the MA is limited to the fitness landscape.
• There is at least one solution in the fitness landscape .
• A fitness function determines the relationship between the fitness of the genotype (or phenotype) and the fitness landscape.
• Selection is based on fitness.

Figure 1: A) Basic lay out of memetic algorithms. A population of individuals is randomly seeded with regard to fitness (initialized). The individuals are randomly mutated and their fitness is measured. Individuals with optimal fitness are further mutated until convergence of a local optima is reached. The process is carried out for the entire initialized population. The global optima is selected from the various local optima. B) Fitness landscape with local optima (A, B and D) and a global optima (C). In a memetic algorithm, the initial population of individual are randomly seeded and can be viewed as any of the arrows indicated in the figure.​

An example of this can be found in Autodock:
Autodock (a molecular docking program) employs MAs in order to try and predict the orientation of a ligand within a protein receptor. A docking run with Autodock can be characterized by the following:

1. Finite fitness landscape: The physical properties of the protein receptor (E.g. electrostatic properties, Van der Waals interactions, desolvation energies etc.). This can be characterized as the pre-existing fitness landscape.
2. Search space: Confined to the protein receptor.
3. At least one solution: The original crystallographic pose.
4. Fitness function: Estimated Free Energy of Binding pose. This is determined through a combination of various interactions including Van der Waals-, electrostatic-, desolvation-, hydrogen bond- and torsional free energy.
5. Selection (guiding function): Selection is based on fitness, i.e. The Estimated Free Energy of Binding pose.

Interestingly, running the software on different occasions result in the convergence of similar ligand poses, even though random variation and selection processes were employed in the algorithm.

Compare this to what science has determined about our existence (discussed here):

Figure 1: Similarities between evolution and a docking simulation.​

There are striking similarities between the development of life on earth and our own designed memetic algorithms. Were do we go from here?

 

[rwenzori]

... as planned.

By whom? Is this more religion in the science section? Should your post therefore be RBPd?

 

[Phronesis]

Interesting article:
Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)

By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize the potential error introduced by horizontal gene transfer. These domains are highly likely to have been present in the Last Universal Common Ancestor (LUCA) based on their universality in almost all of 114 completed prokaryotic (Bacteria and Archaea) and eukaryotic genomes. Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms, supporting the theory that life achieved its modern cellular status much before the main kingdom separation (Doolittle 2000). In addition, we have calculated different estimations of the genetic and functional versatility of all the superfamilies and functional groups in the prokaryote subsample. These estimations reveal that some ancestral superfamilies have been more versatile than others during evolution allowing more genetic and functional variation. Furthermore, the differences in genetic versatility between protein families are more attributable to their functional nature rather than the time that they have been evolving. These differences in tolerance to mutation suggest that some protein families have eroded their phylogenetic signal faster than others, hiding in many cases, their ancestral origin and suggesting that the calculation of 140 ancestral domains is probably an underestimate.

Mmm, "Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms"....

Let's see what they found:
From the conclusion:

From this annotation we know that the LUCA, or the primitive
community that constituted this entity, was functionally and genetically complex (Table 1, Fig. 1, Supplementary Table 3), supporting the theory that life achieved its modern cellular status long before the separation of the three kingdoms.
Contrary to analyses based purely on sequence conservation and universal ubiquity throughout all species, which suggested a simple LUCA with translation and few other genes (Koonin 2003), with the application of a more sensitive method to detect remote homology, we can affirm that the LUCA held representatives in practically all the essential functional niches currently present in extant organisms, with a metabolic complexity similar to translation in terms of domain variety.

What did this primitive clade of LUCAs have? What kind of machinery was present?
1) Replication, transcription, and translation
2) Repertoire of metabolic pathways coupled with the necessary machinery including;

• a) the use of glucose and other sugars
• b) the assimilation of amino acids and nucleosides/ base
• c) the synthesis of ATP both by substratelevel phosphorylation and through redox reactions coupled to membranes
• d) Signal transduction pathways controlling perception.
• e) These pathways are linked to gene regulation and protein modification, protein signal recognition, transport, and secretion, protein folding assistance
• f) And then of course the self-replication machinery.

With all these present in the LUCA, all that is needed is a little time for functional diversification and genetic expansion. The inevitable and repeated emergence of eyes, body plans, toolkits for body plans etc. should not be a problem, even expected if the tape of life was to be replayed even if randomness was taken into consideration.


How deep does the rabbit hole go?

Time will tell I guess....

 

[Phronesis]

Two more articles with fascinating research and results:
A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective

Using an algorithm for ancestral state inference of gene content, given a large number of extant genome sequences and a phylogenetic tree, we aim to reconstruct the gene content of the last universal common ancestor (LUCA), a hypothetical life form that presumably was the progenitor of the three domains of life. The method allows for gene loss, previously found to be a major factor in shaping gene content, and thus the estimate of LUCA's gene content appears to be substantially higher than that proposed previously, with a typical number of over 1000 gene families, of which more than 90% are also functionally characterized. More precisely, when only prokaryotes are considered, the number varies between 1006 and 1189 gene families while when eukaryotes are also included, this number increases to between 1344 and 1529 families depending on the underlying phylogenetic tree. Therefore, the common belief that the hypothetical genome of LUCA should resemble those of the smallest extant genomes of obligate parasites is not supported by recent advances in computational genomics. Instead, a fairly complex genome similar to those of free-living prokaryotes, with a variety of functional capabilities including metabolic transformation, information processing, membrane/transport proteins and complex regulation, shared between the three domains of life, emerges as the most likely progenitor of life on Earth, with profound repercussions for planetary exploration and exobiology.

If you think the LUCA was just a simple self-replicator, think again: From the article the following conclusions were drawn:
The gene content of LUCA with respect to
A) DNA processing (replication, recombination, modification and repair) contains a wide range of functions including;
DNA polymerase
excinuclease ABC
DNA gyrase
topoisomerase
NADdependent DNA ligase
DNA helicases
DNA mismatch repair MutS and MutT
endonucleases
RecA
chromosome segregation SMC
methyltransferase (Epigenetics related enzyme)
methyladenine glycosylase and adenine glycosylase
adenine phosphoribosyltransferase
deoxyribodipyrimidine photolyase
integrase
HAM1 Sir2 involved invarious aspects of genomic stabilit)
TatD—a recently discovered DNase
histone deacetylase (More epigentically related enzymes)

These are just replication related machinery.
Next is:
Transcription/regulation
Translation/ribosome
RNA processing (No, it is not junk DNA, RNA processing was there from the beginnig)
Cellular processes (e.g. cell division control)
Transport/membrane
Electron transport
Metabolism
And several with unknown function...


Second article:
The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner

Background: Since the reclassification of all life forms in three Domains (Archaea, Bacteria, Eukarya), the identity of their alleged forerunner (Last Universal Common Ancestor or LUCA) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? We present a critical survey of the topic and suggest a scenario.
Results: LUCA does not appear to have been a simple, primitive, hyperthermophilic prokaryote but rather a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of moderate temperatures, genetically redundant, morphologically and metabolically diverse. LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from the SSU-rRNA genealogy; consequently, horizontal gene transfer may not have the rampant character assumed by many. Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane, composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion. Bacteria emerged by reductive evolution from LUCA and some lineages further acquired extreme thermophily by convergent evolution. This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from different viral invasions as proposed by Forterre. Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's ancestors having emerged as complex, self-replicating entities from which a genetic code arose under natural selection.
Conclusion: Life was born complex and the LUCA displayed that heritage. It had the "body "of a mesophilic eukaryote well before maturing by endosymbiosis into an organism adapted to an atmosphere rich in oxygen. Abundant indications suggest reductive evolution of this complex and heterogeneous entity towards the "prokaryotic" Domains Archaea and Bacteria. The word "prokaryote" should be abandoned because epistemologically unsound.