Monday, April 10, 2006

'More genes' needed to make life

'More genes' needed to make life, BBC, 3 April 2006, Paul Rincon Scientists trying to make artificial life forms in the lab may have more work ahead of them than they thought. [Thanks to Bill Dembski for alerting me to this. Also at the University of Bath's press release and, but nowhere else as far as I can see, not even Nature which did not mention it both in its Editor's Summary or the abstract of the article! ]

The simplest life forms could require twice as many genes to survive than was previously believed, a research team claims in the journal Nature. [Even the existing ~300 gene minimal genome was an immense problem for evolution, given that unintelligent natural process cannot synthesise even one gene (because the probability of assembling a typical bacterium gene of 1,000 base-pairs is 4-1,000 or ~10-602, i.e. 1 chance in 1 followed by 602 zeros)!

In fact unintelligent natural process cannot assemble even one nucleotide (~1/1000th of a gene):

"Imagining a realistic scenario whereby natural processes may have made proteins on a prebiotic earth-although extremely difficult-is a walk in the park compared to imagining the formation of nucleic acids such as RNA. The big problem is that each nucleotide `building block' is itself built up from several components, and the processes that form the components are chemically incompatible. Although a chemist can make nucleotides with ease in a laboratory by synthesizing the components separately, purifying them, and then recombining the components to react with each other, undirected chemical reactions overwhelmingly produce undesired products and shapeless goop on the bottom of the test tube. Gerald Joyce and Leslie Orgel-two scientists who have worked long and hard on the origin of life problem-call RNA `the prebiotic chemist's nightmare.' They are brutally frank: `Scientists interested in the origins of life seem to divide neatly into two classes. The first, usually but not always molecular biologists, believe that RNA must have been the first replicating molecule and that chemists are exaggerating the difficulties of nucleotide synthesis. ... The second group of scientists are much more pessimistic. They believe that the de novo appearance of oligonucleotides on the primitive earth would have been a near miracle. (The authors subscribe to this latter view). Time will tell which is correct. [Joyce G.F. & Orgel L.E., "Prospects for Understanding the Origin of the RNA World," in "The RNA World," Gesteland R.F. & Atkins J.F., eds. Cold Spring Harbor Laboratory Press, Cold Spring Harbor NY, 1993, p.19]." (Behe M.J., "Darwin's Black Box: The Biochemical Challenge to Evolution," Free Press: New York NY, 1996, pp.171-172)

But these minimal genomes of ~300 genes are all of organisms that are either parasitic (and so use the genome of their hosts to survive), or they can only survive in a laboratory. The minimal genome of free-living (non-parasitic) organisms in nature is ~1,500-1,900 genes (see long `tagline' quote) ]

The "minimal genome" is the least number of genes an organism needs to survive in its environment. [The key words are "its environment". For a parasite that is in its host. Or a laboratory gene knockout experimental organism, it is in that laboratory. It is not the "environment" of the outside world, that the first living organism would have had to survive and reproduce in.]

The traditional way of identifying essential genes may label some as expendable when they are not. A US research team created the world's first synthetic virus in 2002, but scientists are divided about whether viruses are, strictly speaking, alive. [Whether viruses are alive depends on one's definition of life. But one thing all would agree on: viruses, like parasitic bacteria, are not free-living. They need the genome of other organisms to survive and/or reproduce. So the minimal genome of a virus or a parasitic bacterium should include those genes of the host organism which they are dependent on.]

A team at Rockefeller University, US, has created small synthetic vesicles capable of expressing genes that resemble a crude kind of biological cell. [It is interesting that these scientists, with all their combined brainpower and advanced technology cannot make a complete "biological cell", yet they believe that a `blind watchmaker' did it!]

And Dr Craig Venter - the man behind the privately funded human genome sequence - has announced his intention to create a man-made microbe with the minimum number of genes needed to sustain life. [Actually, all that Venter & Co seem to be doing is knocking out genes in real cells and using their cellular machinery. I would like to see him try to make a completely artificial, self-reproducing, self-fuelling, self-repairing cell! A professor of molecular biology wrote at the end of his textbook:

"In these days of astounding advances in science and technology it is perhaps rash to declare dogmatically that anything such as the artificial synthesis of a living cell is impossible. Yet, on what sort of microloom would a biologist weave the membranes of the endoplasmic reticulum, or with what delicate needles could a biologist fashion the intricacies of the cell nucleus?" (Price F.W., "Basic Molecular Biology," John Wiley & Sons: New York NY, 1979, p.466)]

The work in Nature suggests they may have further to go than anyone had predicted. [Quite frankly it is hard to believe that it had not occurred to them that: 1) the first living organism had to be free-living since by definition there was nothing else alive for it to live off; 2) all the minimal genomes they are experimenting with are parasites (and so they are not really minimal genomes when the host genome is factored in - or the genomes of the scientists feeding them nutrients in a laboratory!); and 3) the minimum genome of free-living organisms is at least five times (e.g. Methanococcus jannaschii's 1738 genes) the size of the minimum ~300 genes of parasitic organisms they are experimenting with.]

Scientists identify minimal genomes by removing, or "knocking out", individual genes from a microbe's genome to see what effect this has on its ability to survive. They can then infer which genes are essential to the organism, and which are not, arriving at a minimum number. [That is, "survive" in a laboratory. That a human can "survive" on a heart-lung machine, or a ventilator, in a hospital, does not tell us what are the minimum requirements that humans need to survive in the outside world.]

The authors of the Nature report say this "single gene knockout" method ignores the fact that bacterial cells have back-up mechanisms for synthesising the chemicals they need to survive. [And so a gene could be knocked out and the bacterium could still barely survive on the gene products of another of its genes. But then that knocked out gene really was essential, even though it seemed in the short-term in a laboratory that it was not.]

Researchers from the UK, Hungary and Germany, focused on two evolutionary offshoots of the bacterium Escherichia coli, or E. coli. These offshoots - Buchnera aphidicola and Wigglesworthia glossinidia - have evolved to live inside the aphid and the tstetse fly respectively. [They are both symbiotic parasites that have each lost major sections of their genome, and rely on their hosts' genome to produce the gene products they need. It is a sham to call these minimum genomes without counting the genes in the genomes of their host, that they are dependent on.]

Knowing the metabolic pathways used by E.coli and the lifestyles of Buchnera and Wigglesworthia, the researchers developed a mathematical test to predict which genes these microbes would need to survive in their environments. "We predicted which genes Buchnera and Wigglesworthia might have by just knowing their ecology and what they have evolved from," co-author Professor Laurence Hurst, of the University of Bath, UK, told the BBC News website. "Then we played with another model where we said: 'now we've got loads of nutrients, how small can the metabolism go?'" "The surprise was the metabolism got to be really rather larger than people had suggested the smallest metabolism could be." [There should have been no surprise, given that these are parasitic organisms that depend on their host's metabolism. So this is a another major problem for the origin of the first minimal cell, in that all the evidence is pointing to it being more complex than these minimal parasitic bacteria genomes. See my "The Minimal Cell: A Problem of Evolution 1/2" and 2/2.]

The problem with the single gene knockout method, says Professor Hurst, is that it considers one chemical process at a time, ignoring what would happen if alternative ways of making the same chemical are knocked out simultaneously. As soon as one "metabolic pathway" is removed, the alternative pathway becomes essential. [It will be interesting to see what the revised minimal genome will turn out to be, even for parasitic organisms. Since one would expect that these parasitic organisms would not be carrying much `extra baggage' anyway, I suspect that it will be close to their actual genomes (e.g. B. aphidicola - 580 genes and B. Wigglesworthia - 651 genes). But again that will still not be the minimum genes they need to survive unless their hosts genes they are using is added to theirs.]

Professor Hurst and colleagues suggest single gene knockout studies could underestimate minimal genomes by about 50%. [Since "The minimal genomes published to date range in number from about 260 genes to 670 genes" a 50% increase bumps up the range to 390 - 1,005! Indeed as Bill Dembski observed, the "Origin-of-life problem just went from bad to worse"!]

Dusko Ehrlich, of the Institut National de la Recherche Agronomique in France, who has published a minimum number of genes for the bacterium Bacillus subtilis, said the Nature paper dealt only with a sub-set of the total genes in Buchnera and Wigglesworthia. "The paper deals only with biochemical reactions, not DNA synthesis, protein synthesis, or replication," he explained. [This point is valid only if it is known that there are not back-up genes for those functions, which is possible, given their centrality. But that will only affect the size of the increase, not that there will need to be an increase in the minimal genome necessary for life to exist. Sooner or later (unless they just drop it because they see where it is heading) they are going to come face to face with a minimal genome that is far and away too larger for non-living, unintelligent natural processes to generate. But then one gene (or even one nucleotide) is more than unintelligent natural processes can generate)!]

"They deal with precursors but don't deal with many macromolecules. Many essential genes are required for synthesis of macromolecules. But within what they look at, I don't have a quarrel with. It looks reasonable." ... [So the bottom line, after a bit of quibbling, Ehrlich agrees with Hurst and colleagues' basic conclusion! As their press release's headline says, "Minimal genome should be twice the size, study shows" or as the BBC headline says, "More genes needed to make life"!]

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

"One way to explore the minimum complexity of independent life is to survey the microbial database for the smallest genome. .... The data indicate that the microbes possessing the smallest known genomes and capable of living independently in the environment are extremophilic archaea and eubacteria. ... These organisms also happen to represent what many scientists consider to be the oldest life on Earth. This crude estimate seems to suggest that, to exist independently, life requires a minimum genome size of about 1,500 to 1,900 gene products. (A gene product refers to proteins and functional RNAs, such as ribosomal and transfer RNA.) The late evolutionary biologist Colin Patterson acknowledges the 1,700 genes of Methanococcus are "perhaps close to the minimum necessary for independent life." [Patterson C., "Evolution," Comstock: Ithaca NY, Second edition, 1999, p.23] ... Given the relatively small sample of organisms currently available for assessing life's minimum complexity, investigators may well find the minimum requirement for independent life extends below 1,500 gene products. A newly discovered hyperthermophilic microbe helps establish a lower boundary. This organism, Nanoarchaeum equitans, lives as a parasite attached to the surface of its independently existing hyperthermophile host. Because it is a parasite, N. equitans exploits and depends upon its host cell's metabolism to exist. (In general, parasitic microbes have reduced genome sizes because of their reliance on host cell biochemistry.) Researchers have yet to estimate the N. equitans' genome size, but based on its amount of DNA, its genome size likely falls within the range of about 450 to 500 gene products. Even though incapable of independent existence, N. equitans yields insight into independent life's minimal complexity. Because this parasite thrives with a genome size of about 450 to 500 gene products, the minimum complexity for independent life must reside somewhere between about 500 and 1,500 gene products. So far, as scientists have continued their sequencing efforts, all microbial genomes that fall below 1,500 belong to parasites. Organisms capable of permanent independent existence require more gene products. A minimum genome size (for independent life) of 1,500 to 1,900 gene products comports with what the geochemical and fossil evidence reveals about the complexity of Earth's first life. Earliest life forms displayed metabolic complexity that included: o photosynthetic and chemoautotrophic processes o protein synthesis o the capacity to produce amino acids, nucleotides, fatty acids, and sugars o the machinery to reproduce Some 1,500 different gene products would seem the bare minimum to sustain this level of metabolic activity. For instance, the Methanococcus jannaschii genome (the first to be sequenced for the archaea domain) possesses about 1,738 gene products. This organism contains the enzymatic machinery for energy metabolism and for the biosynthesis and processing of sugars, nucleotides, amino acids, and fatty acids. In addition, the M. jannaschii genome can encode for repair systems, DNA replication, and the cell division apparatus. The genes for protein synthesis and secretion and the genes that specify the construction and activity of the cell membrane and envelope also belong as part of this organism's genome. The discovery of parasitic microbes with reduced genome sizes, like Mycoplasma genitalium, Mycoplasma pneumoniae, and Barrelia burgdorferi (with 470, 677, and 863 gene products, respectively), indicates that life exists, though not independently, with genome sizes made up of smaller than 1,500 genes. These microbes are not good model organisms for Earth's first life forms because they cannot exist independently. But they do have some relevance to life's beginning. These parasitic microbes help determine the barest minimal requirements for life, given that building block molecules (sugars, nucleotides, amino acids, and fatty acids as well as other nutrients) are readily available. Scientists from NIH have used the M. genitalium and H. influenzae genomes to estimate the minimum gene set needed for independent life. These researchers compared the two for genes with common function and reasoned that these constitute the minimum gene products necessary for life. This approach indicated that a set of 256 genes represents the lower limit on genome size needed for life to operate. Using a similar approach, an international team produced a slightly lower minimum estimate of 246. This group developed a universal set of proteins by comparing representatives from life's three domains-eukarya, archaea, and bacteria. In addition to theoretical estimates, researchers have also attempted to make experimental measurements of the minimum number of genes necessary for life. These approaches involve the mutation of randomly selected genes to identify those that are indispensable. One experiment performed on the bacterium Bacillus subtilis estimated the minimal gene set numbers between 254 and 450. A similar study with M. genitalium determined the minimum number of genes to fall between 265 and 350. Random mutations of the H. influenzae genome indicate that 478 genes are required for life in its bare minimal form. The genome of the extreme parasite Buchnera provides another means to determine the size of the minimal gene set. This parasite exists permanently inside aphid cells and has a remarkably tiny genome size. Scientists believe its gene set consists solely of those products essential for life. In contrast, M. genitalium's genome includes genes essential for life and genes that mediate host-parasite interactions. Presumably the genes disabled by mutation eliminated those involved in its host-parasite interactions. The genome size of the Buchnera species varies, with the smallest estimated to contain 396 gene products. Theoretical and experimental studies designed to discover the bare , minimum number of gene products necessary for life all show significant agreement. Life seems to require between 250 and 350 different proteins to carry out its most basic operations. That this bare form of life cannot survive long without a source of sugars, nucleotides, amino acids, and fatty acids is worth noting." (Rana F.R. & Ross H.N., "Origins of Life: Biblical And Evolutionary Models Face Off," Navpress: Colorado Springs CO, 2004 pp.161-163)

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