:: Running from the Thought Police ::

:: Wednesday, March 30, 2005 ::

"We Can't," The Snake Replied, "We're Adders."

::This post is part of the Evolution/ID Correspondence Series::

I'm getting the feeling from his responses that he's getting annoyed with the fact that I refuse to fall to the rusty sword of his illogic. That, or he doesn't like being evangelized himself.

Doug,

It is good that you have made it safely home. Once I send this email I'll go back and forward you the copies of the previous emails that you have lost.

I am well aware of how statistical chances line up. It is your lack of scientific knowledge that gets in the way of your rationally evaluating said chances. That, and you forget that some addition is required for certain statistical events, but I'll get to that in a bit.

First off, cells were not the first forms of life. According to the RNA World hypothesis, RNA (or a related polymer) came first. In order to be self replicating, the first RNA molecules had to be made of the same chiral form and be in a location where there was both a significant concentration of RNA monomers and a temperature high enough to provide the energy to push the reaction forward but not high enough to degrade the polymer. While small, the chances of this happening were not negligible.

Oh, while I think of it, I must remind you that as the monomers of RNA, nucleic acids would have been present by default wherever RNA was.

Right now, the difference between myself, a chem minor, and a chemistry or biochemistry major should be apparent, since they would have the rates of reaction and necessary concentrations on hand and ready to use. All I can say without too much research is that while the chances were small, collisions between molecules occur, even at room temperature, at rates of at least a thousand times a second. As one increases the temperature of a solution, the collisions happen more frequently (temperature being a direct measure of kinetic energy). If such reactions occurred near a thermal vent or, even, in sunlight, adequate energy would've been available for the polymers to form spontaneously. Also, the greater the concentration of reactants (nucleic acids in this case), the more often collisions, orientation-dependent or not, will occur. So, for any given instant, many different nucleotides had the chance of having a collision that caused a bond - and since these are independent of each other, the probabilities have to be added, not multiplied. Then, for a given stretch of time, the probabilities for each given instance also have to be summed. It appears that it is this addition that you primarily overlook.

RNA that self-replicates without help from another molecule is prone to a very high error rate, as there are no mechanisms beyond simple base-pairing to prevent errors from occurring or remaining. The first replicating RNA would then create successor molecules that differed from itself. Eventually, one of these would have been able to, by itself, catalyze (that is, make more energetically - and statistically - favorable) another reaction. Thus, the first ribozyme came into being. Ribozymes, as sequences of nucleic acids that code for a function, are arguably the first genes in this scenario. This ribozyme's target molecule would likely be other RNA, cleaving and/or rearranging it. The chemical descendants of this molecule are with us today, some as introns in yeast genes, others as snRNAs that contribute to mRNA production in our own cells. These exist, so a chemical step (or series of steps) must have occurred to create them. It's but a short step from rearranging RNA to polymerizing (making strands from single units) RNA. As for how proteins got involved, one hypothesis I've run across is that amino acids/peptides were used as markers for specific RNA sequences. Conceptually, a reaction catalyzing the creation of a phosphodiester bond and one catalyzing a phosphate-carboxylic acid bond are not that different, so a mutation in a ribozyme that caused it to favor the latter reaction over the former is not unreasonable, and therefore the chance is not negligible. Again, it is important to note the frequency of mutation in this case (high), the exponentially increasing numbers of RNA strands undergoing mutations (which requires that their individual chances be added together, increasing the chance of single events) and the large timescale involved.

As occasionally happens in biological systems, a system that does one process is reversed to perform a different function. At the chemical level, this is the rule rather than the exception - reactions will go backwards as well as forwards in all but the most energetically unfavorable conditions. At some point, what happened was that a string of amino acids, rather than being easily-identified holders of short strings of RNA, was actually chemically useful in and of itself. This useful peptide/protein could've been one of many things, but what I find likely is that it functioned as a scaffold to hold a ribozyme's RNA in a position to better catalyze its reaction. The string of RNA holding it (the first mRNA) could've been read by the already existing RNA machinery (reversing the reaction, a common chemical and biochemical occurrence). In this "backwards" direction, the ribozyme that assembled the peptide became the first ribosome, a structure upon which all modern life depends. Assuming that this scaffold peptide improved the functionality of the ribosomal RNA (rRNA) and/or any ribozymes functioning as RNA Polymerases, Natural Selection/microevolution enters the picture here (if it hadn't before). An RNA polymerase works better and with greater fidelity, increasing the rate of replication and reducing the amount of mutations. Because mutations were reduced (and deleterious ones discouraged by disfuntionality) only useful protein products (and their mRNAs) would give a reproductive edge. That scientists have created in the lab self-replicating particles consisting of nucleic acids and proteins shows that this is level of life is viable.

I'm honest enough to admit that I don't have the biochemical understanding of the evolutionary history of lipids to give a technical hypothesis. This does not mean that I'm willing to pull an argumentum ad ignorantium argument and say that only God could have done it. I know that some biochemists posit that the above-mentioned particles at some point got trapped in a phospholipid version of a soap bubble. I also know that scientists have also designed self-replicating systems that have a simple phospholipid bilayer.

This gradual development outside of a phospholipid bilayer (read "cell membrane") is not only plausible, but also doesn't require "ALL the cells chemical requirements of and for movement, nutrition, energy, etc. [to] have coalesced inside of a plasma membrane in a chance meeting." As far as we can tell, the first cells were just blobs that divided randomly and the parts that got all the minimal requirements for replication continued to divide. Eventually, some of the scaffold proteins mutated to the point that some became enzymatically active themselves, while others gained the ability to trigger divisions or form other structural functions. Also, at some point, the original RNA genome lost a hydroxy group on its monomers and thus became the more stable, though less catalytically active DNA. The enzyme that did this original encoding of RNA into DNA then had its function reversed (as, again, is biochemically common) and became the first DNA to RNA Polymerase (or, more loosely, an RNA Transcriptase). These other events could have happened before or after reproducing systems were enclosed in a membrane, and are plausible either way.

Going just a bit further, these cells are theorized to have spent about a billion years growing and dividing as just blobs. All the while, every blob with a useful mutation gave rise to two progeny with said advantageous mutation, leading to an exponential increase in the frequency of the mutation - and creating more additive probabilities. Genetic evidence also reveals that a great deal of genomic promiscuity occurred at this time, either through random cell fusions or through more organized events, similar to plasmid transmission in modern single-celled organisms. Meanwhile, intracellular structures developed, and endosymbiosis likely occurred in this time. Remember, a billion years is a very long time for a cell, especially considering that a self-sufficient cell, like E. coli, would be able to grow and divide so often in a couple days that, given enough nutrients, the colony's mass would be greater than the Earth. Once one cell was able to phagocytose (eat) another cell, active competition got a kick-start and the predator/prey relationship has yet to cease since. Inter-organismal relationships put enormous selective pressure on genomes, as not only does a genome (a set of genes in a given cell) have to out produce other genomes, but it has to avoid being destroyed by the products of other genomes as well.

I think that, by this point, I have demonstrated that you need to have concrete numbers before you declare "abiogenesis" to be statistically improbable. At the very least, you need to deal with the exponential increase in instances that occurs with self-replicating molecules and the summing of probabilities that it introduces into your system.

You also seem to not have come across the concept of punctuated equilibrium. On the macro scale, once a species fills a niche well (to the exclusion of any other organism) there's not much pressure on it to change. As a result, evolution "stalls" for a bit where that particular organism is concerned. Small, microevolutionary changes may result (like lactose tolerance) but big things aren't going to happen, especially morphologically (shape-wise). Evolution of that species resumes when either a) a new niche opens up that it can take advantage of, setting up two different populations that can then diverge, or b) a stressor is added to the environment. That stressor might be a major climate change, a new predator, or a new competitor for the same niche. Once such an event occurs, evolution happens fairly rapidly - else the species dies out. This gives rise to a couple of trends. One is what you've noted, that the majority of the fossil record is made up of species without transitory forms. Such transitory forms do exist - go track down an anthropologist and make them talk to you about the mess that is archaic H. sapiens/H. heidelbergensis/H. neandertalensis. The reason we have the fossils to create said mess is related to our immediate ancestors' habit of ritual burial. The second trend is that generalized species tend to have the best long-term success, since it's much harder to un-specialize than it is to either specialize or make a slight change in one's niche.

Punctuated equalibrium is an example of a theory that explains what happens and that makes predictions that one can then test by examining the fossil record. I've yet to see you demonstrate how ID has this ability. My already stated position is that ID, being an invalid hypothesis, can't do this, but I'm still open to reading your attempts to demonstrate otherwise. I'll even give you some instances to explain, as you've been so helpful to do for me in our previous exchanges.

Why do whales have hips?

What good is the Human appendix?

Why is the 16S rRNA common throughout most, if not all, forms of cellular life?

Why do human embryos have tails or gill pouches?

Why are wasps and ants so morphologically similar?

How can microevolution not, in separate populations of the same species, lead over time to macroevolution?

I can think of more, but that's a start.

As you've already figured out, I definitely want to write back - by healing the sick and teaching the ignorant I can protect the otherwise well. You say that you fear the Lord, yet you bore false witness by putting words in my mouth. At no point did I say that Jesus, St. Paul, or any other Apostle, Gospel writer, or Epistle writer was a liar. I did say that Jesus knew that Genesis wasn't literal but would've been called a loony (moreso than he already was) if he had explained science as we now know it. The apostles and everyone else in the time of Christ simply wouldn't have understood it. Newton's laws, heliocentrism, and geologic timescales simply were beyond the scope of what passed as modern thought at the time.

Also, while the Apostles may not have had access to scientific thought and results, they did have the Septuagint, and any close read of Genesis 1-3 easily reveals that it's not literal truth to be taken without contextualizing. How is this evident? Because the sequence of Genesis 2:7,9,19 contradicts the sequence of Genesis 1:11,20-21,24-27. They are two separate accounts and are irreconcilable. They're in there not to convey literal truth, per se, but to explain how things are and why things are. Well-educated Jews living at the time of Christ and immediately afterwards, such as Saul/Paul, would have known this. In fact, I challenge you to find me a passage in the New Testament that references Genesis whose meaning either changes or is significantly diminished by a non-literal reading of Genesis. I fully expect that, just like Matthew 19:4, all the examples you can find fall apart when the passage's larger context is examined.

I revere the Lord. He put together a set of rules and constants for the universe that allow wonderful things such as humans to exist. (The "Goldilocks" universe we live in isn't proof of God, just evidence, by the way.) However, your quote from Proverbs 1:7 is even more easily used against you than against me. You scorn scientific knowledge; you despise the philosophical rebuking of your precious ID, and you resist my instruction. (To make this more plain, philosophy is the systematic exercise of wisdom.) You are the one who, by putting up your fliers, lays "in wait for the honest man" and, "unprovoked, set[s] a trap for the innocent;" to quote Proverbs 1:11. I engage in this so that you can repent of this sin while you can and to protect those who do not have access to the knowledge that I have. As the father forgave the prodigal son so too will our Father forgive your trespasses if you but ask. I cannot stop you from sinning - you're the one who put the noose around your neck, you're the one who has to take it off. I cannot forgive your sins - I do not have that power. All I can do is to play Marley to your Scrooge by helping you to recognize your sin and stop committing it. In that way I may help save your soul and protect others from the consequences of your sin.

Doug, you attempt to lead others astray by your actions, and the more you learn as you correspond with me, the less of an excuse your ignorance becomes. I am generally understanding of the faults of the ignorant and am willing to give the benefit of the doubt. I have decreasing patience for those who should know better. I can only hope that, through the grace of God, the result of our correspondence will be that you will see the folly of your adherence to Sola Scriptura and resultant rejection of evolution. As always, I hope our heavenly Father will bring this to be through His Son, Jesus Christ, who lives and reigns with Him and the Holy Spirit, one God, forever and ever.

[TheSquire]

I truely wonder how long he'll keep up with this. I hope that he'll see the light - though that hope fades with each exchange in which he doesn't admit the fallacy of his positions. Even if he doesn't immediately realize the error of his ways, I have learn much from this and will better be able to cross wits with other IDers in the future.

UPDATE: Doug the creationist really didn't like the last bit. More here.

:: The Squire 2:01 AM :: email this post :: ::
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