So your an Athiest

[AAA]

I very much appreciate that someone is actually answering my questions with specifics. You sound like a busy guy, so if you don't have time to respond then that's fine, but I have some questions.
1. Point mutations (frameshift are a class of this) do not seem sufficient to actually produce new information. The only point mutation that adds new information is a frameshift, and it results if it lands in a protein coding sequence, it results in non-functional protein product due to the fact that it now changes each of the following codons (and therefore amino acids). Do you think point mutations have creative properties?
2. Transposable elements are pre-existing DNA and their insertion into DNA sequences are still not the creation of new genetic information. I still do not see how they could arise by evolutionary means. They have the inverted repeats and genes for proteins for their own removal. How does mutation lead to this type specific DNA sequence? 
3. Aren't recombination events still just the alteration of existing DNA without producing new sequences (I know that it is going to be copied later), but isn't the gene just moving from one homologue to the other?
4. Gene duplication is the most convincing. However, it makes sense to me that having an extra gene would lead to having twice the protein product of that gene, which I feel would cripple the cell's functions and be a waste of resources. If it is a waste of resources than wouldn't it get selected against before it could diverge into a new sequence?

I'm not necessarily trying to convince anyone of anything, I just think intelligent design has been laughed off by the scientific community and I'm not sure why.

No problem. I have a little bit of (much-needed) "downtime" right now, so I'll try.

1) Where do you get the idea that a point mutation is not "new information"? If I change a letter in this sentence, it is new information. If I change a letter in this sentence, it is now information. Just like in the written languages, depending on which base mutates, it can have radical changes on the outcome of the protein produced, and if the mutation occurs in a gene that directs other genes (such as the "Hox" genes), the effects can be radical from a relatively small change. There is zero reason to think that an altered protein would be non-functional; in fact, we observe the opposite of this in nature, in many common proteins (such as hemoglobin), which have a wide range of functional variants. Because a point mutation may alter the amino acid coded for completely, or may insert a "stop coding" codon where Tyrosine used to be (see chart under hide tag), it can change everything.

---

---

2) Transposons interrupt other genes, or they land near other genes which influence one another by proximity (I am sure you will cover this in your genetics textbook), or they induce frame shifts, or a number of other forms of interference. Again, by definition, they alter the information and may produce "new information". Think of them as parenthetical phrases inserted into the middle of a sentence, occasionally into the middle of words. If you th(because of your predjudices)ink that this doesn't change a sentence, you're confused.

3) Yes, except that it's not always 100% accurate, pieces can come off completely, or invert, or a number of other changes. And again, any change in the "wording" of the codon sequence changes the sentence, as far as the chemistry is concerned.

4) There are places in your body where you have 30 or more copies of one gene. If TOO many copies keep being spawned, it can lead to a likelihood of cancers emerging due to problems with regulation of the site, but the short version is that your genes don't make proteins 100% of the time-- they are regulated, switched on-and-off, as needed. If you have two copies, your body can turn them on until the job is done, then turn them back off. But the point, again, is that a duplication (which eliminates almost completely the issue of a mutation damaging the first gene's survival-related job, if it's that kind of gene in the first place) allows for new information because it lets evolution "play" with the duplicate copy to do other jobs. It's how they proved Michael Behe's "irreducibly complex" bacterial flagellum was a bogus claim; they showed where genes had been appropriated from other functional systems in the bacterium to make that motor, etc.

I think if you keep your mind open and ask your professor good questions (after class!), you'll find most of the answers you're looking for are already fairly well-known.

Sorry I took so long to reply... the aforementioned fiancee called me in the middle of typing this to tell me about a problem with our new house in KC, and to drone on about how un-ready our kid is for his part in her church's Christmas play. (Today is dress-rehearsal.)

1. Changing one word to another is making different information, but not new. In order for evolution (molecules to man) to work, you need to actually increase the number of nucleotides, and point mutations don't do that (accept again the frameshift, which I still believe to always disrupt the protein's function). I understand that point mutations aren't always harmful, but every time I try to find examples of beneficial mutations I get something like Sickle Cell Anemia, which decreases the hemoglobin's function in normal conditions. Do you know of any beneficial mutations?

2. We have already covered transposable elements in class, and I'm still not seeing how it is a creative process. It seems to again just be altering existing information. No new nucleotides are being added (unless its a retrotransposon) Your sentence example leads to an inferior sentence after the phrase gets inserted. I have trouble accepting that random nucleotide changes could lead to a sequence for a transposable element, when the odds of getting nucleotides in a functional order seem to be unlikely unless they offer immediate selective advantages (which I don't think the transposons would). Don't you think that the transposons could be seen as a design to allow antibiotic resistance to be transferred among bacteria to keep bacterial populations from being wiped out? This seems like what you would expect from a design given the important ecological role that microbial life plays.

3. I just worry that changing the wording of a sentence is never going to improve the information content of that sentence.

4. If the duplicate genes can be regulated, then does that mean that the promoter and promoter proximal elements  of the gene are also duplicated during the event? Also I think there might be something to the idea of irreducible complexity, because if you have a protein being "played" with by evolution, then it is only going to settle into its role as part of the molecular machine if, when by doing so,  the cell has an improved chance of survival. The cell would not have an improved chance of survival unless the new protein actually had a useful function. The protein changing from one intermediate form over time would have to have a constant use to the cell to not be selected against, right?

And yes, I am trying to stay open minded and I have already talked to my professor about some questions (including the evolution of the tight regulation of the cell cycle). And that's fine, take your time