Another Evolution Question

[LucidDreamer]

Almost all of the energy of life comes from the sun. This energy originates in plants where the energy in light is transformed to chemical energy. The reason this occurs is because light photons excite the electrons of certain molecules in the plants. The plants then pass the electron through various carriers until it creates an electrical potential where ATP is made.

 

So all the energy of life ultimately comes from a simple physical phenomenon where light excites the electrons of atoms into higher energy orbitals. It occurs all the time and not just in life. It occurs in many metals where if a light is shined on them some of the electrons of the individual metal atoms become excited. To see a common example of this just look at your fluorescent light bulb. In this case the electricity is the stimulator instead of the sun. The electricity stimulates the electrons of the atoms in the light bulb and the electrons are excited into a higher energy orbital. Instead of just releasing this energy in the form of heat they release some energy in the form of light. Another example is a meteor. When you see the flash of a meteor its because some of the electrons in the air molecules have become excited and they are releasing energy in the form of light. If the energy that life uses somehow violated the second law of thermodynamics then many other natural physical occurrences must be thrown out as well.

 

The energy that sustains life ultimately results from photoexcitation that occurs all the time in life and in inorganic molecules. The second law of thermodynamics does not state that all forms of energy must immediately go to heat but that it will end up as heat eventually. In fact physics predicts that some energy can and will be transformed into other forms of energy before ending up as heat. One of these forms is the chemical energy of life.

 

That's the first part. The second part of this argument deals with the complex molecules of life being formed. The molecules of life are high energy. This is easy to see when you light a log on fire. All of the heat and light result from the combustion of the log because the log is full of high-energy molecules that release a lot of heat when burned. So why don’t these high-energy molecules violate the second law of thermodynamics? First, when these molecules were created from light energy not all of the energy was turned into the chemical energy of the plant; some was lost as heat. If the plant would have somehow ended up with more energy than the sun gave it then it would violate the first law of thermodynamics.

 

Now, in order to determine whether a reaction is favorable we have an equation called Gibbs free energy. The equation is:G=H-TS or deltaG=delta H-deltaTS. H is energy, S is entropy (second law), T is temperature and not relevant to the discussion and G determines whether the reaction will occur. So whether any given reaction occurs depends upon both energy and entropy. The reactions that produce the complex molecules of life reduce the amount of entropy, which is unfavorable but they make it up by putting in lots of energy. You can produce an endless amount of complex, high-energy molecules in the lab by simply putting in energy in the form of heat or light, etc. These molecules that you make are going against the increase in entropy like the molecules of life but they are still favorable because you put in energy. If the complex molecules of life must somehow violate the laws of entropy then the many reactions that chemist do every day in their laboratory must be declared impossible by the second law of entropy.

 

The ability to produce the molecules of life by combining the atoms that make them up and introducing energy has been demonstrated countless times. Amino acids, urea, and RNA have all been produces with this method. To say that life violates the second law of thermodynamics is the same as saying that you don’t understand the second law of thermodynamics. The simple analogy that entropy is like your room that tends to get messy and unorganized is just a simple way to describe something very complex for early students or laymen. The reaction that is actually used by biochemist and has been proven to be accurate by many experiments is Gibes free energy, which is G= H-TS. By claiming that the high-energy molecules of life should not occur because the entropy is reduced is just simply ignoring one-half of the equation. You cannot just pretend that H is not there and claim that life violates the second law of thermodynamics.

[LucidDreamer]

His second argument was [b']Homochirality somehow arose in the sugars and amino acids of prebiotic soups, although there is no mechanism by which this can occur and is, in fact, prohibited by the second law of thermodynamics (law of entropy). Explain this.[/b]

 

I took a second look at your question and I'm afraid I gave you a very long-winded answer that didn't even answer your question. This particular question is a bit more complicated. In all honesty if you have to defend the pre-biotic soup by explaining how it occurred you’re going to have a very tough time because no one knows. We only know what early life was like from fossil records and fossil records of the pre-biotic soup area are nonexistent so we have to make a lot of assumptions based on what life is like today. Any thoughts about how homochirality or why DNA was chosen or how RNA reproduction started is all speculation. There are no overwhelming arguments for the creation of life on Earth from pre-biotic soup. There is no evidence. For this reason s creationist will try to get you to defend the pre-biotic soup theory and can make very convincing arguments. Your strength lies in the evidence, which starts with from the earliest fossils. You will slaughter someone on argument about the age of the earth. You will most likely win a big-band argument. You can definitely win an evolution argument, starting from the fossil records. You will most likely loose an argument about the pre-biotic soup theory. They will reduce to trying to defend a bunch of baseless theories.

 

First of all, the fact that every living creature has DNA with the same bases, RNA with the same bases, amino acids that are all left-handed, and sugar molecules that are all right-handed is as much an argument for evolution as against it. After all, if a creator made things outright he would not be limited to building on what came before and could use any combination of right and left-handed molecules. However, an organism that has evolved from another would be likely to inherit its predecessor’s characteristics, especially the very basic chemistry. The reason you don't find deviations on the fundamental chemistry like DNA or left-handed amino acids is because so many enzymes, structures, functions, and chemistry depend on them that you would have to change numerous things all at once. Evolution doesn't work this way. It relies upon single mutations. The building blocks are now set in stone for complex organisms and can't be changed.

 

When you test the stability of amino acids you find that the L-handed molecules are more stable, due to weak forces, than the right-handed. In all likelihood this is original reason that all of our amino acids are left-handed now. This explains why they are all left-handed and not right-handed but it doesn't explain why there is homochirality. We don't fully understand this yet but there are several good reasons for homochirality. Several are listed here:

http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v409/n6822/full/409777a0_fs.html

 

I have my own theory for homochirality. During early life, before even the earliest photobacteria, proteins were probably made from only a few amino acids. Perhaps at one time early proto-life only catalyzed the formation of a peptide bond between a few particular amino acids that were formed naturally. Eventually the proto-life developed the ability to synthesize its own amino acids. If this first enzyme that catalyzed the formation of a particular amino-acid formed the L-amino acid than in all likelihood all subsequent enzymes that are formed afterwards by mutations would be forms L-amino acids because enzymes are usually steriospecific (they make only left or right-handed molecules). After all, while there would be a lot of benefit for early life to synthesize three amino acids instead of two there would be disastrous consequences to producing right-handed forms of a particular amino acid because the introduction of right-handed amino acids can cause the protein to be dysfunctional.

 

Another probable cause of homochirality is the machinery that makes the proteins. The units in the cells that make protein are ribosomes. They are RNA and protein conglomerates. The core of the ribosome is a section of RNA that is essential to making proteins. While present RNA molecules are not steriospecific towards making left-handed proteins the early version of RNA that constructed proteins was probably steriospecific towards making L-handed proteins. After much evolution the proteins composed of left-handed amino acids becomes an essential part of the organism. Once the proto-life has reached a certain stage it becomes very difficult to change because so much of the life functions are built around it, sort of like Legos that are built around a certain size of peg. However the RNA molecules are in fact steriospecific towards left-handed molecules when constrained on a monolayer, which is a likely condition of early proto-life. http://www.fasebj.org/cgi/content/full/12/6/503

[LucidDreamer]

And another thing, the second law of thermodynamics has little to do with chirality. Whether a left-handed or right-handed molecule is formed depends upon the particular reaction that forms them in a particular environment. Left-handed amino acids are formed in life because their enzymes control their formation. Racemic mixtures (mixture of right and left-handed) are formed in vitro because the methods used to produce the amino acids have an equal or somewhat equal chance of producing them. Pressures to have an equal mixture of left-handed and right-handed molecules would only occur in the absence of any selective pressures of formation. If there is any advantage to life having homochirality or in the continuation of homochirality then that pressure will determine the likelihood of left-handed or right-handed molecules. Any violation of entropy in the formation of complex, high-energy molecules is overcome by the input of energy.

[Mikel]

Wow, thanks.

[john5746]

Does creationism obey any laws? If the laws aren't important for that theory, why must they be obeyed for any other theory anyway?

[fuhrerkeebs]

Hahahahaha it depends on what type of creationism your talking about. But in General, creationism involves God, and since God is soooo almighty ::cough cough::, there generally aren't too many rules. Hell, there are still people who think God created the earth in 7 days.

[Mikel]

What were the conditions of earth's early atmosphere and why do you think so? Could abiogenesis operate in these conditions? I am wandering because I've been seeing alot of source saying it wasn't after I recieved this post on the Miller-Urey experiments:

It's really an outdated experiment because Miller used a hydrogen rich atmosphere composed of methane, water vapor, and ammonia. It got some immediate publicity because many scientists back then thought that that was what early earth's atmosphere was really composed of. Scientists have rejected it for decades though. Now, early earth's atmosphere is thought to have been composed of nitrogen, water vapor, and carbon dioxide (very little hydrogen involved). The only reason there are still people that come out of college believing it was a legitimate experiment is because many textbooks will still put it in there and treat it very neutrally so as not to support it, but not to convince you it was flawed either.

[Mikel]

He also said this in another post and since I do not know much about nucleotide building blocks I was wandering if one of you could help.

Of the nine general naturalistic predictions for the beginning of life, one states that life gradually appeared on Earth over a long period of time. This prediction is contradicted by the fact that nucleotide building blocks (which are necessary) fall apart quickly in warm (19 days to 12 years) and cold (under 17,000 years) temperatures; destroying both warm and cold origin-of-life models.

Since creationists misrepresent and lie about science often (from what I have seen in the past) what is the truth?

[LucidDreamer]

I would first ask him why he has made it past the age of twelve. If this really did preclude life then he would have died long ago when his nucleotide building blocks fell apart in the warm environment of 98.6 degrees Fahrenheit. In reality he has really made a point for the natural formation of life. This is demonstrated by La Chatleirs rule, which states that a reaction will reach equilibrium in the form of a ratio. So here is reaction 1: unbroken nucleotide block <--->Broken nucleotide block. In reaction 1 the reaction in going both ways and there is an equilibrium that is reached in the amount of unbroken blocks to broken blocks, lets say its broken/unbroken=10/1. Now since we know that nucleotide blocks can form more stable molecules in the form of DNA or RNA (I'm not sure how long DNA or RNA will last in an invitro environment, I think this principle will hold regardless) then we have another equation to add. Here is reaction 2:

Unbroken Nucleotide blocks<---->DNA. This too will form an equilibrium ratio; lets pretend UNB/DNA = 10/1.

 

So since both reaction 1 and 2 establish a ratio and because both reactions share one reactant in the form of unbroken nucleotide blocks then every time a nucleotide is added to a DNA Molecule the first reaction must make another one to replace the one lost and keep a 10/1 ratio. So basically the nucleotides are being remade as they are being destroyed. Also, the first material of replication is believed to be RNA, which is made of Nucleosides not Nucleotides.

[Mikel]

Thanks Lucid. Anyone have a reply to my other post?

[Mikel]

Lucid, he replied when I talked about the 98.6 degree thing. He said

You're kidding right? By the warm prediction, I'm refering to over 200 degrees (F).

Again, I don't know much about this subject.

[LucidDreamer]

Tell him regardless of the temperature the crucial issue is how many nucleotides are being made compared to the amount of nucleotides that are being broken down. Many experiments have shown that organic compounds can be formed from inorganic material. So as nucleotides are broken down they are also formed. It's not like each planet has a select amount of nucleotides given to it and the amount just gets smaller as they break down. Also, remind him that most modern evolutionary biologist believe in punctuated evolution that can occur rapidly. Also Nucleosides of RNA are considered to be the first building blocks of replication. Also there are extremophiles that manage to survive and replicate in very hot temperatures.