:: Running from the Thought Police ::

:: Wednesday, March 16, 2005 ::

Parry, Reposte

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

After receiving Doug's response to my complete takedown of his Creationist flier, I've just finished my response to his rebuttal.

Subject: Re: Intelligent Creator Flier

Doug,

I wonder what your motives are for posting fliers on campus, especially since you appear to not be directly involved with any of the campus ministries or any sort of biological teaching at all. Needless to say, your remaining arguments should be answered.

Oh, I haven't had time today to read through your PDF. I'll get around to it at some point.


You had written quite a bit, but in order no to have an inordinate amount of 'irons in the fire' let me comment on just a few of your statements and you can comment back on them if you wish.

An odd way of conceding my points, but I accept.

You wrote:
Actually, through gene duplication (and divergence), the genome could write itself.

I am talking about initial DNA - not replication of it. Where did it come from? Replication of DNA that is already formed does nothing to answer that question.

You obviously didn't read any of the links I sent you about the "RNA world" hypothesis. DNA came from RNA. RNA either self-assembled, or arose from a proto-RNA.


You wrote in reference to mutations:
Since this is an absolute statement, only one example to the contrary is necessary to discredit it. All mammalian infants possess the ability to produce lactase...

It was written as an absolute statement, but you know full well that the vast majority of mutations are harmful to life and not productive. The example that you gave proves my point. Producing a gene that is eventually repressed is not the same as stating where it came from. So your enzyme example does nothing to prove evolution..

Yes, many are harmful. However, due to the way the triplet code is set up, a good many mutations are silent (producing no phenotypic effect). Some rare mutations are actually beneficial. What you overlook is the phenomenon of enzyme promiscuity. Enzymes - proteins (and some RNA strands) that catalyze reactions - are usually set up so that they catalyze only one reaction or one type of reaction. However, all enzymes have the ability to occasionally, at low frequency, catalyze reactions with other substrates than their normal reaction. Following a gene duplication event, one copy of the gene (and its product protein enzyme) would be able to mutate away from the original action. If one of the promiscuous catalytic activities that enzyme has actually produces something useful for the organism (say, a new type or color of pigment), organisms that further mutated the copy of the gene in ways that made it easier to catalyze the promiscuous reaction would have greater reproductive success, thus spreading the new gene through the population. This would continue until the mutated gene produced a protein that predominantly catalyzed only the formerly-promiscuous reaction, while retaining a copy of the original protein.

Also, you've got my original example backwards - the gene for lactase originally was repressed at age three, but for many modern people this never happens, allowing them to digest dairy products throughout their lifespans. This trait became predominant in populations dependent on herding. This is a textbook example of microevolution.

Remember, I'm not "proving" evolution, I'm defending it. "Proving" evolution is done every day by the scientists who use evolution to further our understanding of the world, from the means by which cells replicate to the mechanisms for bacterial antibiotic resistance. The Modern Synthesis (and its subsequent modifications) provides the basis from which biologists can then investigate life and learn more about it. ID does nothing to provide a platform from which further scientific inquiry can be based.


You wrote:
But complexity, and the coding it is based on, does not evolve.
But it does! The first microprocessor contained only three transistors. Modern microprocessors have more transistors than this country has fingers to count them. Through trial and error, tech companies have managed to increase the amount of processing power in a manner following Moore's law.

Again - this does nothing to prove evolution, but actually is evidence for ID. Tech companies (made up of intelligent - thinking humans) made many, many models NOT by random chance, but by ID! The vehicle that evolution sails round the world on is one of "randomness". As far as you and I know - chemical structures do not exhibit 'thought patterns.' People design things like the microprocessors! They did not come about by time and chance.

Alright, you want a biological example, you'll get one. In order to start the transcription of a gene into RNA (which is the first step in expressing that gene by producing a protein), a number of what are called Binding Factors must associate with the DNA (and each other) in order to recruit RNA Polymerase, which then copies the DNA into RNA, which in eukaryotes is then processed and tossed out of the nucleus into the cytoplasm where it is then translated into a protein. Most binding factors are proteins, though recent research is starting to find small RNA segments that also fill this role. The presence or waspishness of the binding factors themselves is dependent on whether or not they themselves have been produced from their own genes, which are usually turned on or off due to the presence of hormones or other conditions inside or outside the cell. The whole lot of binding factors present in the regulatory region associated with a gene function as a very long series of "IF" arguments, which is followed by the "THEN" of the gene itself. If the gene for one of these binding factors were to be split in a region that divided its functional regions (during a chromosome rearrangement event) and the downstream piece associated with a new promoter, the new gene product (protein) might be able to associate (via Van-der-Waals forces) with the remaining part of the original gene product and so still function in helping to recruit RNA Polymerase to the gene in question. However, because the new gene is associated with a different promoter/regulatory region, the new gene has effectively added a new "IF" argument to the series which is required to cause the gene to be expressed. In this manner, more nuanced expression (and more variously timed expression) can occur, allowing genes to be turned on in precise space-time patterns. To give an example with an easily observed anatomical result, this process, combined with gene duplication, has allowed the HOX gene sequences to change over time, turning fins into limbs and gill arches into a face.

If you had a problem following the preceding paragraph, perhaps you need to take a few more biology classes.


Anyway - I have enclosed the pdf file in my next email. Try not to think 'emotionally' (as it is obvious that you emotions are playing into this), but just consider the evidence for ID. This about the origin of all these systems that you are promoting. How did they form at random?

They didn't form at random - they formed via a very long process in which the rare beneficial mutation added abilities to simple life forms, adding to their complexity through many subsequent generations.

Also, since I demonstrated, clearly and logically, that ID is a scientifically invalid hypothesis, I don't need to consider the "evidence" for it. Besides, the "evidence" isn't evidence at all but merely semantics that misstate modern biological science. Lying and misrepresenting the truth are not only signs that one's arguments are too weak to stand on their own, but are also one of the better ways to get on my bad side.


What about the argument of irreducible complexity? In other words - systems that need ALL the parts together, in the right order, to function at once or else none of them will function at all. (Ie. a microprocessor chip falling into the time of the 1400's will be worthless to that era unless all the parts of a computer are there.)

What about it? It's crap. For example, the Krebs cycle in aerobic cellular respiration would be "irreducibly complex" except for the fact that it exists almost verbatim in most anaerobic bacteria as a set of carbohydrate synthesis pathways, missing only one enzyme to be the complete cycle. Biological systems find ways to combine existing systems into new groupings. Then, through gene duplication (and loss of the original protein in a manner similar to the lactose example discussed before), the new system adapts over many generations into a form that works better together than in the systems of origin, while at the same time obscuring the origins of the system's components. Through comparative genomics, some of these origins can be traced - in fact, most/all (I'm not sure which, molecular biology is a fast-growing discipline) of the "irreducibly complex" systems offered by IDers 10-15 years ago have had their origins explained.

Also, your microprocessor chip analogy helps my point. You're obviously not familiar with the history of computing. While a microprocessor might have been worthless in the fifteenth century, the mechanical looms from the early 19th centry from which all computing is derived would've been manually operatable (with slight, but obvious, modifications) by a weaver in the 1400s. A very clever weaver at that time would've also been able to figure out the card-block system for operating the loom automatically. This is because the mechanical rug and tapestry loom was an early step in the "evolution" of the computer, followed by an electric counting machine used by the U.S. Census in the late 1800s that used punch-cards. The punch-card itself was still in use in the 1970s when my own father, a mathematician, learned how to program computers with them. These punch cards have since been replaced by the keyboard and mouse as programming tools, thus obscuring the computer's textile past. The inventor of the automatic rug and tapestry loom wasn't intending on eventually creating a machine that could do massive simulations (or be used to for word processing, for that matter), all he was looking for was a way to make expensive rugs more efficiently (i.e., to "catalyze" their production).

How did all the parts of a cell just come together one day? Please think about this logically....

I and many other people have thought about this logically. Again, you didn't read the "RNA world" hypothesis stuff I sent you. Admittedly, there are other explanations (the protein-first and lipid/container-first theories, both of which I find lacking), but the "RNA-World" hypothesis currently explains the most and has also predicted new findings, such as the existence of small nuclear RNAs with enzymatic activity. While there are still things to be fleshed out (such as how the ribozymes and amino acids/peptides/proteins got inside a lipid bilayer), the field has advanced far since Miller's Prebiotic Soup experiment in 1953, and will eventually come up with likely sequences and continue to make predictions about what we will find in cells. Admittedly, all our knowledge will be by inference, since individual cells nearly impossible to fossilize - but that hasn't stopped fields like quantum mechanics from making huge strides. Just because science has no current explanation for every detail doesn't mean that we have to throw our hands up, say "God did it." and walk away - which is precisely what ID is.

Your arguments reflect the fact that you do not understand cell biology at a level necessary to summarily dismiss hypotheses. I've shown ID to be faulty, which you've yet to address, and I continue to counter your arguments against evolution. You are ignorant and through ID you attempt to keep other people ignorant as well - something I find most contemptible. I, personally, don't have a right to demand that geocentricism be "rationally considered" just because I can't do the math to personally prove Kepler's theorems about the orbits of celestial bodies. Likewise, I don't see how you can get off railing against evolution, and keeping other people from being properly educated with about it, just because you don't understand molecular biology. I'm really interested in finding out why you're so hell-bent on giving up on developing rational explanations of how life came to be.

[TheSquire]

Note: for anyone wanting to know about some of the stuff I talk about, The Panda's Thumb had posts recently on enzyme promiscuity and the failings of "Irreducible Complexity."

:: The Squire 11:09 PM :: email this post :: ::
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