Posted on 10/19/2006 6:25:16 AM PDT by Grig
WASHINGTON -- Using grammar rules alongside test tubes, biologists may have found a promising new way to fight nasty bacteria, including drug-resistant microbes and anthrax.
Studying a potent type of bacteria-fighters found in nature, called antimicrobial peptides, biologists found that they seemed to follow rules of order and placement that are similar to simple grammar laws. Using those new grammar-like rules for how these antimicrobial peptides work, scientists created 40 new artificial bacteria-fighters.
Nearly half of those new germ-fighters vanquished a variety of bacteria and two of them beat anthrax, according to a paper in Thursday's journal Nature.
This potentially creates not just a new type of weapon against hard-to-fight germs, but a way to keep churning out new and different microbe-attackers so that when bacteria evolve new defenses against one drug, doctors won't be stymied.
Using grammar as their guide, scientists could easily produce tens of thousands of new bacteria-fighters and test them for use as future drugs, said study lead author Gregory Stephanopoulos, a chemical engineering professor at the Massachusetts Institute of Technology.
It would likely take several years to develop the new drugs, but the process conceivably could be speeded up for fighting the worst bacteria, Stephanopoulos said.
In man's war with microbes, bacteria keep mutating to develop resistance to nature-derived drugs. However, this new method could allow scientists to jump several steps ahead of microbes, said Robert Berwick, a computational linguistics and engineering professor at MIT who wasn't part of the team.
Peptides are small proteins that attack the membrane walls of microbes causing it to rupture, said Georgetown University surgery professor Michael Zasloff, who first discovered antimicrobial peptides 19 years ago.
The key turns out to be in the way the peptides are made, which is by stringing together amino acid molecules, which scientists represent with letters. And that's when researchers saw a pattern that would make an English teacher beam.
"You have a string of letters and that string of letters reminds you immediately of a sentence, a kind of incomprehensible sentence, and you wonder in that sentence, 'Is that meaning hidden?'" asked Stephanopoulos. He used the example of a sentence: "Dave asks a question." What Stephanopoulos did was the equivalent of substitute different names for Dave and found that the peptide often still beat the bacteria.
Harvard evolutionary biologist Marc Hauser said that using grammar rules to decode genetics and medicine is growing more popular. But he said he worries that too many people are calling grammar what is really just simple code, not nearly as complicated as human language.
Berwick said the bacteria-fighting grammar rules are equivalent to the extremely basic spelling rule, "i before e except after c." The grammar rules Stephanopoulos developed are about what 2-year-olds learn on their own by listening to adults speak, he said.
the mistake here is that the 'grammar rules' discussed are learned rules. They are not. The authors have discovered new chemistry rules with respect to peptide based antibiotics and 'grammar' is an analogy used to explain these rules to lay people. The intelligence to absorb and understand these rules is our own, not that of the bacteria nor that of the polypeptides involved. At that level, it's just chemicals doing what they do.
Is this really true? Do they actually mutate? Or is it the case that the antibiotic simply wipes out those bacteria that don't have resistance to it, leaving only those that have resistance to multiply? Are we simply doing with bacteria what we do with domesticated plants and animals, selecting for breeding those that have the most of the characteristics we want (except with the bacteria, we are selecting for the characteristics we don't want?
A large part of my previous posts have tried to make the case that there is a lot more than randomness at play. Wasted, apparently.
As part of the quest to synthesize life, research was directed in an attempt to find how few genes it took for a successful bacterium. The answer? 182. Now, I don't think this is quite right because this bacterium is symbiotic, and therefore cannot live without its host. But I'll not complain too loudly on this minor point.
That's a good call on your part, because there are viruses with 4 genes, that also require a host to "live". (Actually, I don't think viruses are "alive" but if they are, they are symbiotic just like the example bacterium above.)
Life is either the result of random events or a deliberate design.
Flase dilemma. There are non-random forces that alter the odds of "survival" of some molecules over others, just like there are forces that alter the odds of survival of some animals over others. This is a part of "molecular evolution" and can be studied in lab.
If science is able to create a living, functioning, bacterium, they will say to creationists: see, you were wrong, we were right. If science is somehow unable to get the bacterium to work, they will never say they were wrong. They will only say they need more time to make it work.
Can you fault them for this? How long should we give them, before faulting them for being unable to explain what happened maybe once only, in all the oceans, over billions of years? Another year or two? Ten? A hundred?
To a person who believes that an outside, sentient, power created life as a deliberate act, how will they react if science is successful? Some will give up that belief. Others will point to the highly improbable nature of the event occurring outside of the determined and ideal lab setting for DNA to spontaneously appear.
I'm not sure you grasp how big the earth is, how long it has been around and therefore how improbable a thing is nevertheless likely to occur. Molecules vibrate about 10^12 times a second, and there are ~3 10^7 seconds in a year, so you have 3 10^9 molecular vibrations in a year. The oceans have been around for ~3 10^9 years, so each water molecule has had the opportunity for ~10^19 vibrations. Now let's go for how many there are. There are 6 10^23 molecules of water in a mole, which occupies 55 mls, A cubic meter has 10^ 6 ml, or 2 10^4 moles, which means about 10^28 molecules in one m^3. But wait, the earth is 70% covered with oceans, about three km deep, and has a radius of ~3000 km. So the area of the earth is 4 Pi r^2, or ~12 x 9 x 10^6 km^2, or about 10^8 km^2. So the volume is this times 3 km deep, x .7 coverage, or about 2 10^8 km^3. Since 1 km^3 is 10^9 m^3, there are 2 10^17 m^3 of water, which are 10^28 molecules each. This means the oceans have about 2 10^45 molecules of water. Now, since each molecule has had ~10^19 vibrations, we're talking about a total of 2 10^64 water-vibrations in all the oceans. That's about how many times molecules have bumped into one another. This number is about 2^212, so to put it in perspective, if you had 212 coins and flipped them all at once, there would be a good chance that ALL of them have come up heads or tails once or twice. Now, admittedly water isn't what makes up DNA, so even if you consider a dilution of a million, a billion, or a trillion for interesting molecules compared to water, there is still an incomprehensibly gigantic number of times these molecules could interact with each other, even a few at a time.
They will point to other issues as well: to the question of matter and energy, to the fact that radioactivity proves there was no past eternity for matter.
It only proves there is no past eternity for the radioactive matter, anyway, but the origin of radioactive elements is known - supernovas.
Both, the reason there are different variants is because they mutate. You can use a single non-resistant bacterium to found an entire colony of which some may be resistant. So when you come to kill em off some may be resistant enough to survive
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