What's the Difference Between a Buckyball and a BMC?
Evolution News & Views January 13, 2016 4:47 AM
We've all seen geodesic domes that were intelligently designed by humans. The inventor, the great designer Buckminster Fuller, might have been quite surprised to learn that nature got there first. Two years after his death in 1983, a new form of carbon was discovered: C60, a geodesic-dome shaped molecule that was named buckminsterfullerene in his honor. Since then, numerous other "fullerenes" have been discovered, comprising shapes of spheres, ellipsoids, and rods. The carbon nanotubes we hear about in electronics are rod-shaped members of the fullerene family. Spherical ones are the most common. Because they look like miniature soccer balls they are often called "buckyballs" for short. The smallest has 20 carbons, but others have hundreds.
Fullerenes can be synthesized in the lab, but some are produced naturally. One can only imagine Dr. Fuller's surprise if he were to learn, while constructing one of his famous domes, that similar structures could be found in his car's tailpipe soot! Natural fullerenes can be produced by lightning, and have been detected in some high-carbon minerals and even in interstellar dust. But now, here's a design-detection puzzle to consider: some geodesic domes are also found in living cells. Is there a difference?
A buckyball's shape is called a truncated icosahedron. Similar icosahedral shapes are widespread in bacteria, where they are called bacterial microcompartments, or BMCs. Some viruses also have icosahedral shapes called capsids. Let's focus on BMCs for now. BMCs are organelles entirely made of protein. They provide a protective shell for various enzymes, and function like membranes, in that they selectively let substances in or out. Interestingly, viral capsid proteins do not appear to have any sequence similarity to BMCs.
Now that we know what BMCs are, how are they formed? Perhaps you expect that we're going to say that they are genetically encoded and constructed by enzymes, so they meet the criteria for intelligent design. Let's not get ahead of ourselves, though. There is some self-assembly involved. A news item from the Lawrence Berkeley National Laboratory says:
Scientists have for the first time viewed how bacterial proteins self-assemble into thin sheets and begin to form the walls of the outer shell for nano-sized polyhedral compartments that function as specialized factories. [Emphasis added.]
The research team spoke of this as "nature's masonry" and "natural origami." They're interested in BMCs because they'd like to imitate them. They'd like to manufacture 3-D "nanoreactors" that can "selectively suck in toxins or churn out desired products." To do that, they first have to understand how bacteria make them. Here's an interesting paragraph:
"We usually only get to see these structures after they form, but in this case we're watching them assemble and answering some questions about how they form," Kerfeld said. "This is the first time anyone has visualized the self-assembly of the facets, or sides, of the microcompartments. It's like seeing walls, made up of hexagonally shaped tiles, being built by unseen hands."
Whoa; that's cool. Sounds like design so far. But we mustn't rush our design inference. What about those buckyballs? Don't unseen hands make them, too? We have to be careful not to personify nature. ID proponents do not conceive of "unseen hands" doing the work of biological design any more than a chemist proposes unseen hands assembling a buckyball.
The building blocks of BMCs are hexagonal proteins. Inside the bacterium, the hexagons assemble into thin sheets like a honeycomb. Because the proteins are convex on one side, and concave on the other, they assemble into spheres. The researchers watched this happen outside the cell:
Liverpool's atomic-force microscope, BioAFM, showed that individual hexagon-shaped protein pieces naturally join to form ever-larger protein sheets in a liquid solution. The hexagons only assembled with each other if they had the same orientation -- convex with convex or concave with concave.
"Somehow they selectively make sure they end up facing the same way," Kerfeld added.
The study also found that individual hexagon-shaped pieces of the protein sheet can dislodge and move from one protein sheet to another. Such dynamics may allow fully formed compartments to repair individual sides.
If we're going to make a design inference, we have to take account of the fact that some natural self-assembly is involved. We need to distinguish between the assembly processes of BMCs and buckyballs to be able to argue that the former are designed and the latter are not. A few months ago we asked, "Are hexagons natural?" Now here's another interesting facet, if you'll pardon the pun: BMCs and buckyballs both have pentagons, too!
Fully-formed 3-D microcompartments have a soccer-ball-like geometry that incorporates pentagon-shaped protein structures known as pentamers, for example, that were not included in the latest study.
"The holy grail is to see the structure and dynamics of an intact shell, composed of several different types of hexagonal proteins and with the pentagons that cap its corners," Kerfeld said.
It's possible that simply adding these pentamers to the protein sheets from the latest experiment could stimulate the growth of a complete 3-D structure, but Kerfeld added, "I wouldn't be surprised if there's more to the story."
You now have the data on BMCs and buckyballs. Could you prove to a skeptic that BMCs give evidence of intelligent design, whereas buckyballs can be explained by natural law? Turn your head away for a minute and think it through before continuing.
We have two similar structures that self-assemble into spherical shapes with facets made of hexagons and pentagons. Why would we infer design for the BMC and not the buckyball? Consider what differentiates the two.
Carbon atoms are all the same (allowing for isotopes). Proteins are not.
The carbons form the vertices of the buckyballs, whereas proteins make up the facets of BMCs.
The proteins in BMCs are made up of amino acids that do not naturally link up into hexagons and pentagons, particularly ones that are convex on one side.
All the amino acids in the proteins are left-handed. There is no known way outside of life to get 100 percent pure homochiral chains of amino acids.
All proteins derive from complex specified information encoded in genes.
The genes for BMC proteins must be translated from one genetic language (DNA) into another (proteins) by means of a symbolic logic system.
The proteins must be folded into their proper orientation upon translation.
The bacterium has to "know" how to get an enzyme inside the BMC, and know which enzyme goes in which organelle.
The resulting BMC is selectively permeable.
Buckyballs don't "do" anything. BMCs have a function that is ensured by assembly instructions, maintenance, and repair systems.
You may be able to add to this list. The point is, you can explain a buckyball by laws of physics and the chemistry of the carbon atom. You cannot explain a BMC from its building blocks. Some amino acids can form naturally, but not homochiral polypeptide chains that perform a function. For that, you need complex specified information and irreducibly complex systems to translate it into functional structures: that is, you need intelligent design.
Those interested in following up on the Lawrence Livermore research can read the open-access paper in Nano Letters. It says very little about Darwinian evolution. Actually, nothing.
Incidentally, the carbon atom is quite interesting, requiring a finely tuned resonance in stars that made Sir Fred Hoyle wonder if someone had monkeyed with physics. But that's another story.
Evolution News & Views January 13, 2016 4:47 AM
We've all seen geodesic domes that were intelligently designed by humans. The inventor, the great designer Buckminster Fuller, might have been quite surprised to learn that nature got there first. Two years after his death in 1983, a new form of carbon was discovered: C60, a geodesic-dome shaped molecule that was named buckminsterfullerene in his honor. Since then, numerous other "fullerenes" have been discovered, comprising shapes of spheres, ellipsoids, and rods. The carbon nanotubes we hear about in electronics are rod-shaped members of the fullerene family. Spherical ones are the most common. Because they look like miniature soccer balls they are often called "buckyballs" for short. The smallest has 20 carbons, but others have hundreds.
Fullerenes can be synthesized in the lab, but some are produced naturally. One can only imagine Dr. Fuller's surprise if he were to learn, while constructing one of his famous domes, that similar structures could be found in his car's tailpipe soot! Natural fullerenes can be produced by lightning, and have been detected in some high-carbon minerals and even in interstellar dust. But now, here's a design-detection puzzle to consider: some geodesic domes are also found in living cells. Is there a difference?
A buckyball's shape is called a truncated icosahedron. Similar icosahedral shapes are widespread in bacteria, where they are called bacterial microcompartments, or BMCs. Some viruses also have icosahedral shapes called capsids. Let's focus on BMCs for now. BMCs are organelles entirely made of protein. They provide a protective shell for various enzymes, and function like membranes, in that they selectively let substances in or out. Interestingly, viral capsid proteins do not appear to have any sequence similarity to BMCs.
Now that we know what BMCs are, how are they formed? Perhaps you expect that we're going to say that they are genetically encoded and constructed by enzymes, so they meet the criteria for intelligent design. Let's not get ahead of ourselves, though. There is some self-assembly involved. A news item from the Lawrence Berkeley National Laboratory says:
Scientists have for the first time viewed how bacterial proteins self-assemble into thin sheets and begin to form the walls of the outer shell for nano-sized polyhedral compartments that function as specialized factories. [Emphasis added.]
The research team spoke of this as "nature's masonry" and "natural origami." They're interested in BMCs because they'd like to imitate them. They'd like to manufacture 3-D "nanoreactors" that can "selectively suck in toxins or churn out desired products." To do that, they first have to understand how bacteria make them. Here's an interesting paragraph:
"We usually only get to see these structures after they form, but in this case we're watching them assemble and answering some questions about how they form," Kerfeld said. "This is the first time anyone has visualized the self-assembly of the facets, or sides, of the microcompartments. It's like seeing walls, made up of hexagonally shaped tiles, being built by unseen hands."
Whoa; that's cool. Sounds like design so far. But we mustn't rush our design inference. What about those buckyballs? Don't unseen hands make them, too? We have to be careful not to personify nature. ID proponents do not conceive of "unseen hands" doing the work of biological design any more than a chemist proposes unseen hands assembling a buckyball.
The building blocks of BMCs are hexagonal proteins. Inside the bacterium, the hexagons assemble into thin sheets like a honeycomb. Because the proteins are convex on one side, and concave on the other, they assemble into spheres. The researchers watched this happen outside the cell:
Liverpool's atomic-force microscope, BioAFM, showed that individual hexagon-shaped protein pieces naturally join to form ever-larger protein sheets in a liquid solution. The hexagons only assembled with each other if they had the same orientation -- convex with convex or concave with concave.
"Somehow they selectively make sure they end up facing the same way," Kerfeld added.
The study also found that individual hexagon-shaped pieces of the protein sheet can dislodge and move from one protein sheet to another. Such dynamics may allow fully formed compartments to repair individual sides.
If we're going to make a design inference, we have to take account of the fact that some natural self-assembly is involved. We need to distinguish between the assembly processes of BMCs and buckyballs to be able to argue that the former are designed and the latter are not. A few months ago we asked, "Are hexagons natural?" Now here's another interesting facet, if you'll pardon the pun: BMCs and buckyballs both have pentagons, too!
Fully-formed 3-D microcompartments have a soccer-ball-like geometry that incorporates pentagon-shaped protein structures known as pentamers, for example, that were not included in the latest study.
"The holy grail is to see the structure and dynamics of an intact shell, composed of several different types of hexagonal proteins and with the pentagons that cap its corners," Kerfeld said.
It's possible that simply adding these pentamers to the protein sheets from the latest experiment could stimulate the growth of a complete 3-D structure, but Kerfeld added, "I wouldn't be surprised if there's more to the story."
You now have the data on BMCs and buckyballs. Could you prove to a skeptic that BMCs give evidence of intelligent design, whereas buckyballs can be explained by natural law? Turn your head away for a minute and think it through before continuing.
We have two similar structures that self-assemble into spherical shapes with facets made of hexagons and pentagons. Why would we infer design for the BMC and not the buckyball? Consider what differentiates the two.
Carbon atoms are all the same (allowing for isotopes). Proteins are not.
The carbons form the vertices of the buckyballs, whereas proteins make up the facets of BMCs.
The proteins in BMCs are made up of amino acids that do not naturally link up into hexagons and pentagons, particularly ones that are convex on one side.
All the amino acids in the proteins are left-handed. There is no known way outside of life to get 100 percent pure homochiral chains of amino acids.
All proteins derive from complex specified information encoded in genes.
The genes for BMC proteins must be translated from one genetic language (DNA) into another (proteins) by means of a symbolic logic system.
The proteins must be folded into their proper orientation upon translation.
The bacterium has to "know" how to get an enzyme inside the BMC, and know which enzyme goes in which organelle.
The resulting BMC is selectively permeable.
Buckyballs don't "do" anything. BMCs have a function that is ensured by assembly instructions, maintenance, and repair systems.
You may be able to add to this list. The point is, you can explain a buckyball by laws of physics and the chemistry of the carbon atom. You cannot explain a BMC from its building blocks. Some amino acids can form naturally, but not homochiral polypeptide chains that perform a function. For that, you need complex specified information and irreducibly complex systems to translate it into functional structures: that is, you need intelligent design.
Those interested in following up on the Lawrence Livermore research can read the open-access paper in Nano Letters. It says very little about Darwinian evolution. Actually, nothing.
Incidentally, the carbon atom is quite interesting, requiring a finely tuned resonance in stars that made Sir Fred Hoyle wonder if someone had monkeyed with physics. But that's another story.
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