(April 9, 2016 at 5:24 pm)AAA Wrote: I know how they theorized it happens, but just assuming the scaffolding that you're talking about ever existed is highly speculative. How did the enzymes get there? 'well other enzymes that were less developed morphed into them over time'. How did it survive before it had a mechanism to accomplish the regulation? 'well these other enzymes could regulate it too, but they were simpler and less intricate'. I read an article a few weeks ago about how catalytic promiscuity may aid enzymes in their evolution. One of the many speculations that they made were that enzymes with < 10% amino acid similarity were closely related because they shared the sequence for an active site. 


And I genuinely have no idea what you are talking about with the chemical reactions done hundreds of times to show polypeptide formation. Forming nucleotides or amino acids is NOT the same or equivalent to forming a functional sequence of them. And nobody is saying that you couldn't simplify the biochemical pathway a little, but you would really have to do some mental gymnastics to try to get it reasonably simple for the mechanisms of evolution to be sufficient.

Dafuq are you talking about? We know that the "scaffolding" systems exist because we can find the roots of the evolutionary changes/shifts in populations that are closely related (in which the systems did not change, or the scaffolding did not fall away), just as we can still find the roots of the evolution of the nephridic system, the deuterostome digestive system, the eyes, the brain, etc., all still extant in living populations. Similarly, we can track the DNA patterns mathematically and SEE (map) how they changed with time... System A duplicated into A and A1, then A1 mutated into the basis for an entirely different system, before finally System B1 took over with a more-efficient version, etc etc. This is what they mapped when Behe claimed the bacterial flagellum was IC, discovering that, no, the systems he said IC were in fact useful in their "disassembled" form, working as cellular pumps before being co-opted into part of the "motor" for the flagellum. Surely you've read that paper.

Working from principles we know and understand about how DNA functions is not mere speculation. 

And what do you mean, "...for the mechanisms of evolution to be sufficient"? All it takes for evolution is to have a self-replicating molecule form. One. Something akin to "Hammerhead" RNA/ribosome, for instance. The Jet Propulsion Lab folks in the Ames Research Center over at NASA have been working on figuring out the conditions under which we'd expect to find (aside from earth) environments which can produce these substances from the precursor molecules found in interstellar ice clouds. If I recall correctly, they are examining the possibility that life here didn't begin with RNA (though the "RNA World" hypothesis seems to hold the most weight, at the moment), but with TNA, based on the simpler molecule threose... though, given the fact that we've found ribose in interstellar ices via radio telescope and duplicated its formation in labs, it may not have been necessary for the simpler molecule to prestage RNA.

So why don't you just pick up the phone, call the astrochemists at the Ames Research Center, and tell them that they're totally off-base? I'll get the number for you:

(650) 604-5000 NASA Ames Research Center

(April 9, 2016 at 10:40 pm)Goosebump Wrote: So, isn't this good evidence of evolution? Doesn't it take the theory and put it into law? Or is that never possible? Rather, why is evolution still just a theory when we can see it now with super duper microscopes and such?

Respectfully, you have a (common) misconception about the term "theory", as used in science. In the common vernacular, "theory" means a hunch or a guess. In science, it is the highest praise that can be given to an idea which is a successful and well-demonstrated predictive model of how the laws come together to make a particular phenomenon happen. Laws are "just" observations of a single phenomenon which seems to happen the same way, every time... for instance, the Law of Gravity says "mass attracts mass". The Theory of Gravity (which is significantly less-well-understood than the Theory of Evolution, I should add) explains why this might be so.

The United States National Academy of Sciences defines scientific theories as follows:

The formal scientific definition of theory is quite different from the everyday meaning of the word. It refers to a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence. Many scientific theories are so well established that no new evidence is likely to alter them substantially. For example, no new evidence will demonstrate that the Earth does not orbit around the sun (heliocentric theory), or that living things are not made of cells (cell theory), that matter is not composed of atoms, or that the surface of the Earth is not divided into solid plates that have moved over geological timescales (the theory of plate tectonics)...One of the most useful properties of scientific theories is that they can be used to make predictions about natural events or phenomena that have not yet been observed. (From https://en.wikipedia.org/wiki/Scientific_theory)

(April 9, 2016 at 10:40 pm)Goosebump Wrote:

(April 9, 2016 at 10:09 pm)TheRocketSurgeon Wrote: The evolution of bacteria under the fierce Natural Selection pressures imposed by our antibiotics has become a major issue in hospitals, as resistant strains of Staphylococcus aureus (among others) have become effectively immune to anything we can throw at them. https://en.wikipedia.org/wiki/Methicilli...cus_aureus

As you noted, viruses evolve quite rapidly, due to the relative simplicity of their genomes, but we understand their evolutionary pathways pretty well--that's what the numbers in the H1N1 (etc.) Influenza virus refer to. In fact, because the Flu virus evolves as it moves from its origin in birds to pigs to humans, we look at the genome of the virus that appears each year in order to get ahead of manufacturing a vaccine that will impact the human version when it emerges. Sometimes we get it partially wrong, as occurred a couple of years ago, and the companies must scramble to make enough of the "right" version. It's why you must get a new flu shot every year; the old one usually won't work on next year's version, because it will have evolved.

It's also one of the major reasons people still die of HIV, despite highly-effective antiviral medicines; the virus population "learns" (by the deaths of those that have the wrong genome to resist the medication, leaving only the resistant ones to breed) to resist the cocktail being taken by the patient.

So, isn't this good evidence of evolution? Doesn't it take the theory and put it into law? Or is that never possible? Rather, why is evolution still just a theory when we can see it now with super duper microscopes and such?

There is no disagreement that this developed resistance actually occurs. The debate is whether the mechanism by which they develop it is a mechanism that can be applied to the development of all biological features. Bacterial resistance is usually the result of the cell gaining new genetic information that was already in existence. It takes up sequences from viruses (transduction), from its environment (transformation), or from other bacteria (conjugation). These new sequences allow it to survive. These aren't all the ways that they develop resistance, but in these examples there is no new genetic information being produced, it is just acquiring helpful genes it found in its environment. It seems that there are a lot of pre-existing mechanisms to keep bacterial populations alive. This may signify the ecological importance of such organisms. Life does not want us to get rid of them, probably for our own good. The fact that there are antibiotic resistance genes already in existence could be interpreted as a part of a design that intended to make bacterial/viral populations strong.  

And technically it is never possible to move it into law, but it can reach a point where it is unreasonable to reject it (which I don't think it is at that point). The reason people who are aware of this still debate evolution is because the way that they develop resistance is likely not sufficient to explain the origin of other biological systems.

Um... what do you mean "no new genetic information"?

Where do you think the biosynthetic pathway to digest nylon was co-opted FROM!?

ETA: Also... do you seriously not understand the difference between "law" and "theory" in science?!? Your statement, above, seems to indicate that you don't. Theories don't get "promoted" into laws. Theories are made up of laws.

The problem is that theists of a certain caliber hardly understand anything about real science due to the fact that they think placing the word creation in front of science magically makes them understand science.

(April 9, 2016 at 10:48 pm)TheRocketSurgeon Wrote:

(April 9, 2016 at 5:24 pm)AAA Wrote: I know how they theorized it happens, but just assuming the scaffolding that you're talking about ever existed is highly speculative. How did the enzymes get there? 'well other enzymes that were less developed morphed into them over time'. How did it survive before it had a mechanism to accomplish the regulation? 'well these other enzymes could regulate it too, but they were simpler and less intricate'. I read an article a few weeks ago about how catalytic promiscuity may aid enzymes in their evolution. One of the many speculations that they made were that enzymes with < 10% amino acid similarity were closely related because they shared the sequence for an active site. 


And I genuinely have no idea what you are talking about with the chemical reactions done hundreds of times to show polypeptide formation. Forming nucleotides or amino acids is NOT the same or equivalent to forming a functional sequence of them. And nobody is saying that you couldn't simplify the biochemical pathway a little, but you would really have to do some mental gymnastics to try to get it reasonably simple for the mechanisms of evolution to be sufficient.

Dafuq are you talking about? We know that the "scaffolding" systems exist because we can find the roots of the evolutionary changes/shifts in populations that are closely related (in which the systems did not change, or the scaffolding did not fall away), just as we can still find the roots of the evolution of the nephridic system, the deuterostome digestive system, the eyes, the brain, etc., all still extant in living populations. Similarly, we can track the DNA patterns mathematically and SEE (map) how they changed with time... System A duplicated into A and A1, then A1 mutated into the basis for an entirely different system, before finally System B1 took over with a more-efficient version, etc etc. This is what they mapped when Behe claimed the bacterial flagellum was IC, discovering that, no, the systems he said IC were in fact useful in their "disassembled" form, working as cellular pumps before being co-opted into part of the "motor" for the flagellum. Surely you've read that paper.

Working from principles we know and understand about how DNA functions is not mere speculation. 

And what do you mean, "...for the mechanisms of evolution to be sufficient"? All it takes for evolution is to have a self-replicating molecule form. One. Something akin to "Hammerhead" RNA/ribosome, for instance. The Jet Propulsion Lab folks in the Ames Research Center over at NASA have been working on figuring out the conditions under which we'd expect to find (aside from earth) environments which can produce these substances from the precursor molecules found in interstellar ice clouds. If I recall correctly, they are examining the possibility that life here didn't begin with RNA (though the "RNA World" hypothesis seems to hold the most weight, at the moment), but with TNA, based on the simpler molecule threose... though, given the fact that we've found ribose in interstellar ices via radio telescope and duplicated its formation in labs, it may not have been necessary for the simpler molecule to prestage RNA.

So why don't you just pick up the phone, call the astrochemists at the Ames Research Center, and tell them that they're totally off-base? I'll get the number for you:

(650) 604-5000 NASA Ames Research Center

I don't think it's a given that once you have a replicating system you have unlimited capacity to develop everything else. All we see in extant species are systems that can accomplish their task. In order to get from any system to another, you have to have functioning system at every step. Are you telling me that you believe there are different functioning systems going from (lets pick the brain) the most primordial nervous system to the higher evolved ones? Think of all the systems that would have had to exist in between. Is it not speculative to say that they existed? 

Also no I don't want to tell them they are off base, I never said that we should stop origin of life research. I look forward to seeing what they find. I don't discourage investigation into a scientific idea.

(April 9, 2016 at 10:55 pm)TheRocketSurgeon Wrote:

(April 9, 2016 at 10:40 pm)Goosebump Wrote: So, isn't this good evidence of evolution? Doesn't it take the theory and put it into law? Or is that never possible? Rather, why is evolution still just a theory when we can see it now with super duper microscopes and such?

Respectfully, you have a (common) misconception about the term "theory", as used in science. In the common vernacular, "theory" means a hunch or a guess. In science, it is the highest praise that can be given to an idea which is a successful and well-demonstrated predictive model of how the laws come together to make a particular phenomenon happen. Laws are "just" observations of a single phenomenon which seems to happen the same way, every time... for instance, the Law of Gravity says "mass attracts mass". The Theory of Gravity (which is significantly less-well-understood than the Theory of Evolution, I should add) explains why this might be so.

The United States National Academy of Sciences defines scientific theories as follows:

The formal scientific definition of theory is quite different from the everyday meaning of the word. It refers to a comprehensive explanation of some aspect of nature that is supported by a vast body of evidence. Many scientific theories are so well established that no new evidence is likely to alter them substantially. For example, no new evidence will demonstrate that the Earth does not orbit around the sun (heliocentric theory), or that living things are not made of cells (cell theory), that matter is not composed of atoms, or that the surface of the Earth is not divided into solid plates that have moved over geological timescales (the theory of plate tectonics)...One of the most useful properties of scientific theories is that they can be used to make predictions about natural events or phenomena that have not yet been observed. (From https://en.wikipedia.org/wiki/Scientific_theory)

So theories and laws aren't the same. There can't be a "law" of evolution even with the observable evidence of evolving bacteria and viruses etc? There could be a law of flu virus always evolving to fucks up our noses. But that wouldn't be the same as a theory? Am I remotely in the ball park of understanding this?

(April 9, 2016 at 11:12 pm)TheRocketSurgeon Wrote: Um... what do you mean "no new genetic information"?

Where do you think the biosynthetic pathway to digest nylon was co-opted FROM!?

ETA: Also... do you seriously not understand the difference between "law" and "theory" in science?!? Your statement, above, seems to indicate that you don't. Theories don't get "promoted" into laws. Theories are made up of laws.

I said no new genetic information meaning no new or even variations of genes for those three types of resistance developed. There is just a difference in what organisms contain them. 

And I don't know how nylonase was formed, but I bet it wasn't mutation or a gene duplication. It was probably just a different organization of existing proteins that allowed it to do it. I'm not too familiar with it, so sorry if that is way off. 

And I seriously do understand it. You should read it again. It says "and technically it is NEVER possible to move it into a law". Don't put words in my mouth. I never said the word promote. I said it can reach a point where it is unreasonable to reject it.

(April 9, 2016 at 11:48 pm)Goosebump Wrote: So theories and laws aren't the same. There can't be a "law" of evolution even with the observable evidence of evolving bacteria and viruses etc? There could be a law of flu virus always evolving to fucks up our noses. But that wouldn't be the same as a theory? Am I remotely in the ball park of understanding this?

There are many laws contained within the Theory of Evolution. One of the most common is the law known as Natural Selection (co-discovered by Charles Darwin and Alfred Wallace), which states that the gene-sets within a population which are more "successful" (in that they survive to produce children and grandchildren at a higher survival rate than their fellows within the population) will increase the percentage of those genes found within the population, and thus the population will evolve in the "direction" of those genes. Another is the law of genetic inheritance, which states that offspring will mainly (along with "edits" provided by new mutations occurring with each generation) contain the DNA of their ancestors/parents, but will not be duplicates or blends of those parents, as Gregor Mendel discovered with his pea plants.

A law is an observed phenomenon which always occurs and can be described (usually mathematically), such as the Law of Gravity stating that mass will attract mass in proportion to the size of those masses and their proximity (and in the case of a large, nearby mass like the earth, will result in us falling "down" toward the center of that mass). The formula for that attraction is:



(F, the force of gravity, is equal to the two masses multiplied with each other and the Gravitational Constant, G, divided by the square of r, the distance between the center of those masses.)


The Theory of Gravity, which is actually several competing theoretical models (none of which quite agree with one another), attempts to explain why that occurs-- that's why it was such a big deal to have possibly/probably discovered the Higgs Boson, a particle that confers said gravitational attraction between matter.

https://en.wikipedia.org/wiki/Quantum_gravity

The attempts to resolve the conflicts between these theories, all of which accurately describe part of what occurs with gravity but which cannot be made to reconcile with one another (in much the same way that the Mercatur projection and the Conic projections of the globe both give different pictures, but are attempts to describe the same phenomenon-- the earth's land masses)... the search for a unifying theory for all forces between atoms/particles is called the Theory of Everything, and solving it is one of the major objectives of physicists today (thus all the giant particle colliders being built).

(Edit To Add: I mention the Theory of Gravity because no one questions the existence of gravity, or the phenomenon described by the Law of Gravity, but it is in fact significantly less well-understood and -supported than the Theory of Evolution.)

(April 9, 2016 at 11:55 pm)AAA Wrote: And I don't know how nylonase was formed, but I bet it wasn't mutation or a gene duplication. It was probably just a different organization of existing proteins that allowed it to do it. I'm not too familiar with it, so sorry if that is way off. 

A "different organization of existing proteins" is exactly the phenomenon I've been describing, by which mutations allow existing systems to shift to a new task (a problem which gene duplication makes much easier, since the un-mutated version of the gene keeps right on doing what it was doing within the cell, while the new variant performs a new task).