Wednesday, March 08, 2006

An article of relevance: Essential genes of a minimal bacterium #1


My apologies for the delay in responding to your comment. Because of something you didn't say, but I thought you said, about the complexity of cyanobacteria. This coincidentally is exactly where I am up to in the first draft of my book "Problems of Evolution", in Chapter 11, "Major Transitions," "11.1 Non-living to prokaryote" (some chapters differ from my webbed Table of Contents). So, I decided to respond in a blog post. But it became so long, I had to break it into two parts. It is part two (which I have not yet finished) which is perhaps the more interesting part. My words are in bold to distinguish them from yours.

Joe G said...

JG>An article of relevance:
Essential genes of a minimal bacterium

Thanks. I had already cited it:

"Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. Using global transposon mutagenesis, we isolated and characterized gene disruption mutants for 100 different nonessential protein-coding genes. None of the 43 RNA-coding genes were disrupted. Herein, we identify 382 of the 482 M. genitalium protein-coding genes as essential, plus five sets of disrupted genes that encode proteins with potentially redundant essential functions, such as phosphate transport. Genes encoding proteins of unknown function constitute 28% of the essential protein-coding genes set. Disruption of some genes accelerated M. genitalium growth." (Glass J.I., et al., "Essential genes of a minimal bacterium," Proceedings of the National Academy of Sciences, USA, Vol. 103, No. 2, January 10, 2006, pp.425-430)

in my post, "Re: Improbability of Abiogenesis Calculations (A Response to Ian Musgrave)" and included it in my "Problems of Evolution" book outline, PE "The minimal cell Minimum number of genes".

JG>That is quite a bit of CSI & IC to account for.

Agreed. And this was for a parasitic bacterium, Mycoplasma genitalium, which depends on the gene products of its host organism (in this case us) to survive. For a free-living bacterium, the minimum number of genes is ~1500-1700:

"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. ... 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. 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 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).

Yet there is no naturalistic process which can create from non-living chemicals even one gene! In fact, there is no naturalistic process which can create from non-living chemicals even one nucleotide!:

"In the 1980s a scientist named Thomas Cech showed that some RNA has modest catalytic abilities. Because RNA, unlike proteins, can act as a template and so potentially can catalyze its own replication, it was proposed that RNA-not protein-started earth on the road to life. Since Cech's work was reported, enthusiasts have been visualizing a time when the world was soaked with RNA on its way to life; this model has been dubbed `the RNA world.' Unfortunately, the optimism surrounding the RNA world ignores known chemistry. In many ways the RNA-world fad of the 1990s is reminiscent of the Stanley Miller phenomenon during the 1960s: hope struggling valiantly against experimental data. 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] Even if the miracle-like coincidence should occur and RNA be produced, however, Joyce and Orgel see nothing but obstacles ahead. In an article section entitled "Another Chicken-and-Egg Paradox" they write the following: `This discussion ... has, in a sense, focused on a straw man: the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA s catalytic potential.... Without evolution it appears unlikely that a self-replicating ribozyme could arise, but without some form of self-replication there is no way to conduct an evolutionary search for the first, primitive self-replicating ribozyme.' [Joyce & Orgel, 1993, p.13] In other words, the miracle that produced chemically intact RNA would not be enough. Since the vast majority of RNAs do not have useful catalytic properties, a second miraculous coincidence would be needed to get just the right chemically intact RNA." (Behe M.J., "Darwin's Black Box: The Biochemical Challenge to Evolution," Free Press: New York NY, 1996, pp.171-172)]

JG>As I like to remind people-If life didn't arise from unintelligent, blind/ undirected (non-goal oriented) processes, there would be no reason to infer that its subsequent diversity arose solely due to those type or processes.

Agreed. If the intervention of an Intelligent Designer/Creator is the inference to the best explanation for the origin of life, then that should be accepted. And then the existence of that Intelligent Designer/Creator should be the new starting point in revaluating the evidence of the subsequent history of life. In that case it would still be possible that the Intelligent Designer/God thereafter worked solely through natural processes, but that should be decided on the evidence not on scientists' personal religious (or rather anti-religious) preferences (especially if they were wrong on the origin of life).

JG>And as they say in Maine "You cahn't (can't) get heah (here) from theah (there)", meaning even with "descent with modification" there isn't anything that can be modified in the alleged LUCA to allow it to give rise to the diversity we see today.

Disagree (if I understand you correctly). Since I accept common ancestry, I also accept that there was a Last Universal Common Ancestor (LUCA) and therefore that that LUCA's descendents underwent "descent with modification" to give rise to the diversity we have today. However, that does not mean that that "descent with modification" was fully naturalistic (see above).

JG>Heck we can't even conduct Dr. Behe's proposed "evolving a bacterial flagella experiment".

Well, for all their hot air, no evolutionist has yet been prepared to take up Behe's challenge: "Q. [Mr Muise] Now another complaint that we've heard in the course of this trial is that intelligent design is not falsifyable. [sic] Do you agree with that claim? A. [Prof. Behe] No, I disagree. And I think I further in slides from my article in Biology and Philosophy in which I wrote on that. If you get to the next slide -- oh, I'm sorry. Thank you. You got that. In this, I address it. I'm actually going to read this long quotation, so let me begin. Quote, In fact, intelligent design is open to direct experimental rebuttal. Here is a thought experiment that makes the point clear. In Darwin's Black Box, I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can't be produced by natural selection acting on random mutation, or any other unintelligent process. To falsify such a claim, a scientist could go into the laboratory, place a bacterial species lacking a flagellum under some selective pressure, for mobility, say, grow it for 10,000 generations, and see if a flagellum, or any equally complex system, was produced. If that happened, my claims would be neatly disproven. Close quote. So let me summarize that slide. It says that if, in fact, by experiment, by growing something or seeing that in some organism such as a bacterium grown under laboratory conditions, grown for and examined before and afterwards, if it were seen that random mutation and natural selection could indeed produce the purposeful arrangement of parts of sufficient complexity to mimic things that we find in the cell, then, in fact, my claim that intelligent design was necessary to explain such things would be neatly falsified. Q. I got a couple questions about the proposal that you make. First of all, when you say you place something under selective pressure, what does that mean? A. Well, that means you grow it under conditions where, if a mutation -- a mutant bacterium came along which could more easily grow under those conditions, then it would likely propagate faster than other cells that did not have that mutation. So, for example, if you grew a flask of bacteria and let them sit in a beaker that was motionless, and the bacteria did not have a flagellum to help it swim around and find food, they could only eat then the materials that were in their immediate vicinity. But if some bacterium, some mutant bacterium were produced that could move somewhat, then it could gather more food, reproduce more, and be favored by selection. Q. Is that a standard technique that's used in laboratories across the country? A. Yes, such experiments are done frequently. Q. And I just want to ask you a question about this grow it for 10,000 generations. Does that mean we have to wait 10,000 years of some sort to prove this or disprove this? A. No, not in the case of bacteria. It turns out that the generation time for bacteria is very short. A bacterium can reproduce in 20 minutes. So 10,000 generations is actually, I think, just a couple years. So it's quite doable. Q. Have scientists, in fact, grown bacteria out to 10,000 generations? A. Yes, there are experiments going on where bacteria have been grown for 40,000 generations. So again, this is something that can be done. Q. So this is a readily doable experiment? A. That's correct." (Behe M.J., "Tammy Kitzmiller, et al. v. Dover Area School District, et al.," Transcript, October 17, 2005, Morning session)

JG>Also I have an issue with pathogens being any UCA, for obvious reasons.

It would not have been a pathogen back then, since there was nothing else for it to be a pathogen of (except perhaps other bacteria which have since become extinct).

[To be continued in part #2]

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


Joe G said...

You are on no schedule to respond to my rants. That you responded at all is good enough. Thank you.

Common ancestry- I have read most of what you posted in your essay. Obviously I missed (didn't read) some of your other work or I would have (and should have) realized you already discussed the "Essential genome of minmal bacterium". My apologies for that.

My point is what can be modified in a population of "bone-less" inverts that would give rise to "boned" vertebrates?

The only answer I ever get is "DNA!", which I say is a bogus "answer".

But hey I am the lunatic who favors "alien" colonization for the original populations of organisms on this planet. And even though that just "pushes things back" I say that science has to go with what we have and keep searching for more. IOW solve OUR reality then figure out the next step.

Off topic:
But here is a serious question- DNA replication and transcription-

When the DNA is "unzipped" an existing "stock-pile" of nucleotides is used to make the necessary copy (either of the entire sequence or the "gene").

Where does that "stock-pile" come from? I can't find it in any biology literature.

Anonymous said...

Just curious, how do you apply selection pressure to evolve a flagellum? Specifically, how would you physically set up the experiment? Beyond the "Put some bacteria in there that can survive better to compete with them and then wait 10,000 generations." How can you physically do this experiment? If intelligent design/creation can hold up to this, then intelligent design scientists need to create and do these experiments, and then publish them in the scientific literature. The idea behind hypotheses being falsifyable is that you actually try to falsify them. It is not enough to simply criticize the research and ideas of others-- that is what politicians do and it is obviously not productive.

Stephen E. Jones said...


Thanks for your comment.

>Just curious, how do you apply selection pressure to evolve a flagellum?

ID does not claim that "selection pressure" alone would "evolve a [bacterial] flagellum". It is *Darwinists* who claim that the natural selection of random (i.e. undirected) mutations (NSRM) evolved the bacterial "flagellum". So it is up to Darwinists to explain how "selection pressure" of random mutations *could* plausibly, and then *did*, "evolve a [bacterial] flagellum."

>Specifically, how would you physically set up the experiment? Beyond the "Put some bacteria in there that can survive better to compete with them and then wait 10,000 generations." How can you physically do this experiment?

See above. Since it is a *Darwinist* (not an ID) claim, your question should be directed to Darwinists.

>If intelligent design/creation can hold up to this, then intelligent design scientists need to create and do these experiments, and then publish them in the scientific literature.

First, why the double-standard? It is *Darwinists* who claim that "selection pressure" *did* "evolve a [bacterial] flagellum." So why should not *they* be required to experimentally test their claim?

Second, unlike the Darwinists, ID has no public funding, no research facilities and no access to "the scientific literature." However, if Darwinists were willing to transfer some of their public funding and research facilities to enable ID scientists to experimentally test ID's claim that it requires the input of intelligent design "to evolve a [bacterial] flagellum," and grant them access to "the scientific literature" to report the commencement, progress and results of that experiment, then I am sure the ID movement would be only too happy to carry out this experiment!

>The idea behind hypotheses being falsifyable is that you actually try to falsify them.

Agreed. See above on ID being willing, subject to being given adequate publicly funded resources, to "actually try to falsify" Darwinists' claim that NSRM was sufficient to "evolve a [bacterial] flagellum," by demonstrating that even with the input of intelligent design how difficult it is to do.

But again why the double-standard? Why are *Darwinists* exempt from testing their *own* "hypotheses" by trying to falsify them, specifically their claim that the natural selection of random mutations *could* (and *did*) "evolve a [bacterial] flagellum"?

>It is not enough to simply criticize the research and ideas of others-- that is what politicians do and it is obviously not productive.

Actually, in the real world, most of science *does* involve "simply criticiz[ing] the research and ideas of others." There is little or no public funding available for scientists to re-run experiments to test the results of other scientists' experiments.

Especially in the situation where there is little or no actual Darwinist "research" *to* "actually try to falsify."

In particular, "research" involving experimentally testing, in an attempt to falsify, the Darwinist hypothesis that the bacterial "flagellum" *was* evolved by "selection pressure" of random (i.e. undirected) mutations.

Stephen E. Jones