Science News

[Gumpngreen]

Ask your "buddy" what he thinks of this article:

http://www.taemag.com/issues/article...cle_detail.asp

[wgjones3]

his last words, which I know will hold 'special meaning' for you were, "...If you continue on the creationist tract, then of the two of us, professionally speaking, only one of us is going to walk away from this..."

At least he knows and has admitted that you're gonna win this debate

[Gumpngreen]

In her inimitable way, Science reporter Elizabeth Pennisi has once again portrayed a scientific controversy undergoing active ferment. This time it’s about the evolutionary origin of cell nuclei, which she terms “specialized, DNA-filled command centers.� At the conclusion, she gives prominence to a “provocative, but circumstantial and controversial� suggestion that viruses taught cells how to wrap their DNA in double membranes with controlled access. Since the idea presupposes that viruses preceded all three domains of life – prokarya, eukarya and archaea – “If this is true, then we are all basically descended from viruses,� as a believer puts it. The idea is unpalatable to some. “I do not believe [it],� a German molecular biologist retorts. “The idea of the viruses ‘inventing’ [eukaryotic cells] from scratch is hard for me to conceive.�
Pennisi treats the new viral theory as tentative at best. What’s more revealing in her article are the problems with previously-popular ideas, and why. According to her, the key insight at a meeting in France last month on the subject was: “They had underestimated the complexity of the eukaryotic cell’s 1.5-billion-year-old [sic] precursor. The data presented indicated that this ancestral cell had more genes, more structures, and more diverse biochemical processes than previously imagined� (Emphasis added in all quotes.) For a glimpse why, look at Pennisi’s brief description of the nucleus:

Each nucleus in a eukaryotic cell consists of a double lipid-based membrane punctuated by thousands of sophisticated protein complexes called nuclear pores, which control molecular traffic in and out of the organelle. Inside, polymerases and other specialized enzymes transfer DNA’s protein-coding message to RNA. Other proteins modify the strands of RNA to ensure that they bring an accurate message to the ribosomes outside the nucleus. The nucleus also contains a nucleolus, a tightly packed jumble of RNA and proteins that are modified and shipped out of the nucleus to build ribosomes.

Eukaryotes are distinguished from bacteria by their double-membrane nuclei. “The nuclear distinction between prokaryotes and eukaryotes shaped early speculation about the development of complex life,� Pennisi says about ideas floating around up to the 1970s. Some thought eukaryotes were evolved prokaryotes, and others thought prokaryotes were degenerate eukaryotes. But then Carl Woese created new woes by identifying bacteria-like cells that were distinct from both prokaryotes and eukaryotes: so different, in fact, to warrant classification in their own domain – archaea. Others soon were surprised to find that eukaryotes appeared to have genes from both bacteria and archaea.
So another story was born, the endosymbiont or merger hypothesis. This proposed that eukaryotes arose from “the ancient symbiotic partnership between bacteria and archaea.� That theory came under fire from the discovery of faint but distinct nuclei in an unusual group of bacteria, named planctomycetes, that live in soil and fresh water. Some of these planctomycetes have organelles and double-membraned sacs of DNA and RNA. According to a critic of the merger model, these observations “turn the dogma that ‘prokaryotes have no internal membranes’ upside down� Now, it seems no one is sure which way is up.
There’s more to cause vertigo for evolutionists: the complexity of the nuclear pore complexes (NPCs). “Explaining these structures has always posed a sticking point for nuclear evolution [sic].� For one thing, “without pores, the nucleus can’t function.� But for another thing, Pennisi continues, the same planctomycetes, and possibly some other archaea and prokaryotes, apparently possess structures resembling these complex traffic-control gates. “Bacteria with nuclear pores and internal membranes, features typically considered eukaryote-specific, suggest that the nucleus was born much earlier than traditionally thought.�
For some, that leaves as the leading contender the controversial theory that viruses first invented the nucleus. This, however, only pushes the complexity of nuclei and their pores farther back in time, and foists a huge design problem on earth’s most primitive biological entities. That is why the molecular biologist quoted earlier can’t believe that simple viruses created such complex structures from scratch. Pennisi shares a few speculations, based on circumstantial evidence, how it might have happened. But when she ends by pushing the answer to the future, it underscores the fact that no current theory accounts for the origin of the nucleus:

Did a virus provide [sic] the first nucleus? Or was it something an early bacterial cell evolved [sic], either on its own or in partnership with an archaeum? To resolve the origin of the nucleus, evolutionary biologists are exploring new techniques that enable them to determine relationships of microorganisms that go much further back in time....

The biologists in France argued and discussed many ideas. “But when it came to accounting for how the nucleus was born,� Pennisi admits, “no single hypothesis bubbled to the top.� She quotes French molecular biologist Patrick Forterre who said, “It’s like a puzzle. People try to put all the pieces together, but we don’t know who is right or if there is still some crucial piece of information missing.�

http://www.sciencemag.org/cgi/content/full/305/5685/766

[Merry]

I've heard zero-population growth types refer to mankind as a virus upon the earth, so I'm sure they'll love this. (Even Prince Philip once said if he could he'd like to come back as a virus to help kill off 'excess' humans. Maybe he'll consider himself as having 'arrived.')

And if we are basically, a virus, created in the image of God, then it's like calling God a disease. Which, could be what some of these brilliant people think, anyway.

[Gumpngreen]

ATP synthase, the miniature rotary motor that powers our cells, has been a subject of great interest since the elucidation of its rotary function won three scientists a Nobel prize in 1997. As an example of a precision-crafted, true electric rotary motor in living systems (another being the larger bacterial flagellum), it also provides a classic case study in intelligent design vs. evolution. It has been the subject of frequent updates in these pages. Now, another discovery about this ATP-synthesizing engine has revealed a deeper level of fine tuning. Japanese scientists publishing in PNAS found a precision coupling between two components that was unexpected, yet apparently essential.
For review, recall that ATP synthase has two functional domains, named F0 and F1. The F1 part that actually synthesizes ATP from ADP + P is now fairly well understood. It is composed of three pairs of lobes that spring-load ATP with every 120o turn of the camshaft, each pair of lobes either loading, catalyzing or ejecting an ATP molecule. The F0 domain, however, has been harder to study. Scientists knew it looks like a carousel of identical proteins, labeled c subunits. Linked to it is a camshaft, named the gamma subunit, that drives the synthesis of ATP in F1. Scientists knew the F0 carousel runs on protons delivered by a gumball-like mechanism named the a subunit. But up till now, they were not sure how many c subunits comprised the carousel – or even if the number mattered. Some studies had hinted that the F0 motor contained anywhere from 8 to 13 c subunits, depending on the species. Now, the team of Mitome et al. found the answer: it is 10, and it must be 10 and only 10. Other numbers don’t work. That’s strange. It means that F0 needs 10 protons per revolution, but F1 produces 3 ATP per revolution. The ratio 10:3 is not an integer. How can that be?
The scientists arrived at the number 10 by customizing F0 rings with fixed numbers of c subunits, 2 through 14. Then they linked them to the F1 domains and watched how much ATP was synthesized. Results were obtained for only c=2, 5, and 10, which is interesting, considering that 2 and 5 are factors of 10. The c=2 and c=5 cases produced a little ATP, and c=10 produced the maximum. All the other numbers produced none. The team deduced, therefore, that 10 (or one of its factors) is essential to match the proton-loading mechanism of the a subunit.
The scientists also measured the proton flow through their custom carousels when disengaged from F1 and found, again, that 10 was the only number that worked. Without 10 c subunits, no protons flowed. Divide a circle of 360o by 10, and you get a 36o angle per c subunit during a complete revolution of the F0 motor. The F1 domain, by contrast, produces ATP for each 120o turn, or 3 ATP per complete revolution. The scientists seemed surprised that the proton-ATP ratio, “one of the most important parameters in bioenergetics,� is not an integer. It’s as if three protons are sufficient to generate an ATP sometimes and four other times, because one cannot have a third of a proton. Wouldn’t it be more logical if the number of c subunits was a multiple of three, say 6, 9, or 12? With c=9, for instance, the camshaft angle would regularly line up with the F1 lobes every 3 protons, yielding one ATP every time, nice and neat. The fact that it does not means that the coupling between F0 and F1 is not strict, as with toothed gears, but “permissive� – as if the two domains rotate according to their own structural needs, and are coupled together by a adaptor mechanism that has some degree of freedom to either twist or slip.
The scientists ruled out slippage. They knew that the camshaft can only produce an ATP in the F1 domain when it is lined up perfectly at the 120o steps. Instead, they found that there is enough elastic flexibility in the camshaft to permit twist up to 40o during its rotation. This flexibility allows the two domains to work separately, each according to its optimum configuration, with the twisting camshaft able to rock back and forth a little to give the F1 lobes time to complete their work. In scientific lingo, “The flexibility of gamma allows both the F0-gamma and F1-gamma interfaces at the free-energy minima to stay in conformations adequate for the proton transport in F0 and the catalysis in F1 despite the step-size mismatch, providing sufficient time for those events to take place.� (Emphasis added in all quotes.)
One more thing. There isn’t much tolerance for error in this system. The team found that a single point mutation at a spot named E56 in the c subunit was enough to quench all proton flow and all ATP synthesis: “This result provides evidence that each of all 10 E56 in the c-ring is indispensable.� Also, the quantity of 10 subunits in the c-ring is critical, because 8, 9, 11, 12 and other numbers did not fit the gumball proton-delivery system of the a subunit: “Thus, the proton transport through F0 requires very strict arrangement of contact surface between F0-a and F0-c in the F0 assembly and even a rotary displacement as tiny as 3.3o (360o / 10 – 360o / 11) seems to be enough to disable a proton transfer between them.�
The team made their measurements on ATP synthase motors from a species of thermophilic (heat-loving) bacteria. They feel they have found a coupling strategy in living systems that could demonstrate a general principle: “Here, we report the permissive nature of the coupling between proton transport and ATP synthesis of F0-F1, but such nature of the coupling can be general among other biological motor systems to connect critical well tuned microscopic events in the large domain motions.�

This discovery reveals a deeper level of design even more difficult to explain by evolution. (As expected, these authors make no reference to evolution in their paper.) A simple, easy-to-fathom machine would use the integer ratio; 3 protons yields one ATP. The 10:3 ratio, puzzling at first, actually shows superior engineering. It enables two disparate components with different operational requirements to be coupled together for the maximum efficiency of each. In software, it would be like the driver that allows a device to work with any operating system. In hardware, it would be like a tractor with a power-takeoff adapter that allows the engine to operate an attachment running at a different RPM.