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Author Topic:   Definition of Species
herebedragons
Member (Idle past 53 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 72 of 450 (543960)
01-22-2010 11:15 AM
Reply to: Message 69 by RAZD
01-07-2010 9:30 PM


Re: Speciation discussion, expectations and reality
Hi Razd. Now it's my turn to apologize for taking so long to respond.

How much more change is needed?

Needed for what? To convince me that the ToE is accurate and is the best explanation for life on this planet? To convince me that creation is a myth? Or that God doesn't exist? Or simply to convince me that organisms change over time?

I am convinced that organisms change over time. It's obvious they do. What I am not convinced of is the extent of change. Fish --> Amphibians; Theropods --> Birds; Chimps --> Humans. Now be honest, just based on what we've discussed so far would it be enough to convince you if you were skeptical? I don't know how long you have been studying evolutionary biology, but it is obvious that you have a lot of knowledge on the subject and it may be hard for you to see this from my point of view. But I am having a hard time taking observed evolution and extrapolating that into the kind of changes mentioned above. (note that I am still investigating and learning about this, not declaring victory or proclaiming that the ToE is false)

One of the major things I am having the hardest time wrapping my mind around is the idea of random mutations being the source for new biological innovations. Let's consider the example of E. coli bacteria developing a new metabolic pathway. Here is my paraphrase of how it happens. E. coli is introduced to an environment with a food source that it normally does not metabolize. During the first several hundred generations, random mutations are occurring until at about 400 generations it hits on one that improves its ability to metabolize the new food source. It can then metabolize the new food source and grow at a normal rate.

I picture a "random mutation generator" functioning much like a program they use in movies to decode passwords, trying thousands of combinations until one works. Maybe this isn't very realistic, but still, there would be literally thousands, maybe hundreds of thousands, of mutations that could occur until by chance it stumbles upon the right mutation that works. This seems to me highly improbable and I don't think we observe the rate of mutation that would be needed to make it realistically probable. I don't think it was discussed how many times the experiment was repeated, but I assume the experiment is repeatable with the same general results, which makes the probability that this would happen randomly over and over even more unlikely.

Additionally, I saw no mention of any other mutations that occurred during the study. The only one that was noted was the metabolic pathway. The law of probability would dictate that other mutations are just as likely to occur, even when you take selection into account. I am sure neutral mutations did occur, but there must be other beneficial mutations that could have occurred instead of, or in addition to, the metabolic pathway mutation. When the experiment is repeated, you should see other randommutations occuring.

Another problem I have is that in nature the environment would not likely be stable enough to give the organism time to come up with a mutation randomly. The levels of the food source would fluctuate and other environmental forces would compete for the organisms "attention".

All in all, the probability that this pathway evolved randomly seems mind boggling to me. And that's just a fairly simple (biologically speaking) change. The probabilities increase exponentially with more and more complicated systems requiring many different cell structures and proteins and such.

A more likely explanation would be that the information for the new pathway was already contained in the genome and the change in environment caused it to be turned on like a switch. I would be interested to know if the E. coli that had developed the new pathway could go back to using the original pathway. Would it have to re-evolve by random mutations? Or does it still exist in the coding?

The variation in dog breeds and the B. oleracea species would be another indication of this. There are large amounts of morphological differences and yet very little genetic distance. This would indicate that the information was already contained in the DNA and selection merely changed what genes were expressed. What happened with the silver fox also supports this. First of all, the trait for tameness did exist in the silver fox population (they selected for the tamest individuals - although in this case tameness is a relative term). Secondly, after they managed to tame the population (domesticate) they exhibited many of the same complementary traits that dogs exhibit. Is this a coincidence? What are the chances that this was random? It seems highly, highly improbable to me. Ancestry could explain it, but enough genetic variation should have accumulated to make it somewhat less likely that they would exhibit similar complementary traits.

We do know mutations occur as we can observe them and do comparative studies, but do we truly know the source of these mutations? Why do genes mutate? Are they random or driven by environmental forces? Or maybe both with less emphasis on randomness.

I admit that I only know enough about genetics to make myself look foolish and I need to do much more research on the subject. But, from what I have read so far on evo-devo and epigenetics it seems to have the potential to be revolutionary to evolutionary science. I also might add, somewhat hesitantly, that if IDers and creation scientists would get involved in this kind of science (or any science for that matter) it may have the potential to revolutionize their claims too.

Well, I don't have any more time right now, but hopefully by the next time I post, I will be able to talk a little bit more intelligently about the genetic issues I brought up.

Again, thanks for your time and patience in discussing this with me.

Take care


This message is a reply to:
 Message 69 by RAZD, posted 01-07-2010 9:30 PM RAZD has responded

Replies to this message:
 Message 73 by greyseal, posted 01-22-2010 4:01 PM herebedragons has not yet responded
 Message 74 by Wounded King, posted 01-22-2010 4:42 PM herebedragons has not yet responded
 Message 75 by RAZD, posted 01-22-2010 7:56 PM herebedragons has responded
 Message 83 by barbara, posted 07-23-2010 1:11 PM herebedragons has not yet responded

  
herebedragons
Member (Idle past 53 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 78 of 450 (546097)
02-08-2010 11:08 AM
Reply to: Message 75 by RAZD
01-22-2010 7:56 PM


mutations, possibilities and opportunity
Hi Razd. I hope you’re feeling well. Just a quick post so you know I haven’t given up on this and to clear up a couple of points.

No need, this pace suits me, and it allows for digestion of information before proceeding to the next level, and better understanding of your concerns.

Good. I like the pace too. I don’t like to have to wade through numerous personal attacks and senseless arguments to learn anything. This is why I would rather keep our discussion here as long as it is relatively on topic - the mechanisms that cause change and the effect of those changes. Is that OK?

I am quite busy right now, so a slower pace is easier to manage. It might interest you that I am taking a Botany course at a local university. The course does cover evolutionary theory somewhat, though we won’t focus on it. Later in the year we cover genetics and heredity but mostly as an overview. I am considering getting my degree in biology or biochemistry or maybe microbiology. If this discussion accomplishes nothing else it has renewed my love for science.

The rest will be for you to decide,

You are right. It all comes down to each of us needs to choose what we believe. I probably shouldn’t have responded the way I did, but I felt the question “how much more change is needed?” was a bit condescending and begged a ”needed for what?” reaction. I do feel an obligation to accept evidence from observation, what I do not feel obligated to is interpretation of those observations.

it can be due to ignorance of the actual possibilities, or just being uninformed.

I can admit my ignorance and being uninformed; however, I feel the need to not just accept information verbatim, but to think about it, analyze it and make sense of it.

however please note that I am a Deist, not an atheist

Just out of curiosity, what is a Deist? Do you believe that some unknown deity set up the natural laws, started life and has left it to it‘s natural course without interference? Not meant to be a theological discussion, I just have never met anyone that said they were a Deist before and was curious.

OK, now back to the discussion ...

The major source of mutations is imperfect replication: during reproduction the DNA of the parent is imperfectly replicated in the cells for the offspring.

I understand that the rate of error in DNA reproduction is 1 error in 100,000,000 base pair replications (that’s conservative toward the more error end). Then after replication and before the cell actually divides, it is checked for errors and repaired as needed. Repair mechanisms probably don’t detect point mutations very efficiently, but would repair larger damage. Of course repair mechanisms are imperfect too and would allow errors to progress through division occasionally. Then, as you noted, the error must happen within germ cells. (I have read that bacteria are able to turn off their DNA repair mechanism when environmental stress levels rise). This is what gives me the impression of improbability.

This is a common argument from improbability

I think part of the problem here is my understanding of “random”. Random is defined as: “without an identifiable pattern, plan, system or connection”.

That something is "mind boggling" is not any criteria on which to base a scientific conclusion (else much of physics and chemistry would be discarded),

The difference is physics and chemistry and very predictable. There is nothing “random” about chemical and physical reactions. As “mind boggling” as these interactions are, they behave predictably and with identifiable patterns and connections. One criterion for scientific conclusions is repeatability. Would “randomness” be repeatable? Example (I will stick with the E.coli experiment for now): If the first experiment showed mutation conferring benefit after 400 generations but the next trial resulted in the extinction of the colony, would that not invalidate the experiment as being unrepeatable? Do I misunderstand the concept of repeatability? Repeatability is based on the fact that natural laws are predictable.

I want to clarify my thinking (not my position at this point) about this “unknown mechanism”. I am not saying there is anything “magic” and I don’t believe I said “hidden DNA”. I think you misunderstood what I was saying. What I am trying to consider and was asking you to consider is more of a cause and effect situation. I don’t see that DNA replication errors can account for necessary mutations at least as the cause of them. The “randomness” doesn’t seem to fit with the cause and effect observations we make in nature. Weather appears to be random, as it can vary from day to day, but we know that weather is “caused” and it “affects” future weather occurrences in a complicated, interactive system of natural processes. Do living cells operate under different principles?

I have class shortly, so I need to get going. But, next time I would like to discuss the E.coli experiment a bit more. I did not see some of the observations you discussed in the article I read. Could you give me a link to a good article on the experiment? It would save me a lot of time searching. What I didn’t see in the article I read was any results from subsequent experiments. Did they repeat the experiment and get identical results or did they get a totally different outcome? I also didn’t see that they were able to identify any individual organism that the mutation started from, but that the colony suddenly experienced rapid growth. Did the colony that began the growth contain individuals with the mutation and without the mutation? The individuals without the mutation would not necessarily have died out, as they were surviving before the mutation. I also don’t recall that the beneficial mutation had built upon a previous neutral mutation, but we could be talking about two different studies.

Well, take care and I’ll talk to you later

Thanks


This message is a reply to:
 Message 75 by RAZD, posted 01-22-2010 7:56 PM RAZD has responded

Replies to this message:
 Message 81 by RAZD, posted 02-09-2010 10:17 PM herebedragons has not yet responded

  
herebedragons
Member (Idle past 53 days)
Posts: 1513
From: Michigan
Joined: 11-22-2009


Message 79 of 450 (546253)
02-09-2010 2:33 PM
Reply to: Message 75 by RAZD
01-22-2010 7:56 PM


mutations, possibilities and opportunity continued
Hi again, Razd.

I had a few minutes and I wanted to expand on my previous post a bit.

Everything that happens within a cell is highly organized and incredibly precise. Cells take in materials, synthesize proteins and other compounds, expel waste and produce energy in precisely the amounts needed. Out of hundreds of theoretically possible amino acids that could exist, only 20 are used for building proteins. And these are arranged in exactly the correct order and in exactly the proper quantities for sustaining the organism. E.coli bacterium have 600 to 800 proteins active at any one time and complex multi-cellular organisms have several thousands. Each protein has a specific function and is specifically suited for that function. Cells have an elaborate system of communication that allows substances to move throughout the organism precisely where they are needed. As I am sure you are well aware, this list could go on and on. The organization and precision of living systems is incredible (to say the least)!

Then from that knowledge and observation (or despite it), we introduce the mechanism for adaptation as a random, undirected process. The process that allows organisms to change in order to meet changing demands of their environment is based on blind chance and failure of a highly ordered system to function correctly. We have an extremely precise and ordered system relying on luck for its survival. This is the premise of evolution. Organisms change in response to environmental pressures. They don’t change for just no reason, otherwise there wouldn’t so much stasis in the fossil record. Coleanthus is a simple example. Why didn’t this species change over millions of years? It didn’t need to. It was perfectly adapted to its environment. The only way organisms survive drastic changes in climate or environments is if they are lucky enough to acquire a chance, random mutation that impart a beneficial characteristic that gives it a better chance of survival.

What I am saying is that this doesn’t make sense to me. The problem with supposing a mechanism that is not random is that you can’t go very far with it before you are forced to conclude that some intelligence designed it. And the science community will have no part of that. I, however, do not have those same limits.

Again, what I am suggesting is that perhaps, the mechanism for change is not random and undirected, but in fact, controlled by the cell. The cells genetic structure has certain built in “adaptation” mechanisms that allow the organism to change in response to its environment. That such mechanisms exist is a fact.

http://www.textbookofbacteriology.net/regulation.html

Bacteria can change protein structures, patterns, enzymes, and other regulation compounds to respond to environment. They can regulate metabolic pathways by turning metabolite production on and off depending upon the substrates available in the environment. They can change their gene structure, control the rate and process of transcription, alter proteins after synthesis and adjust the translation of proteins. Bacteria are able to respond to extreme variations in environments.

How can we observe and acknowledge the above and then conclude that the mechanism the brought all that about is random and undirected? Don’t tell me there is no other known mechanism. If I said abiogenesis could not be true because no know mechanism exists, the response would be that just because we haven’t identified the mechanism, doesn’t mean it can’t be possible.

You asked how it is even possible. I understand that something like 97% of the human genome is non-coding information. It used to be referred to as “junk DNA” as it was thought to have no purpose. It is now known that it has purpose and I think somewhere around 60% has an identifiable purpose. It involves transcription, regulation, expression, development and much more. But there is still a large amount of genetic information that is unclear about what purpose it serves. Perhaps the answer lies within the “unknown” - it usually does.

Again, I am not saying this is my “position”, but merely my thoughts. This is an argument of improbability, but more thought out. It’s more than just saying it's too “mind boggling” to accept. It’s improbability based on observations. I’ve mentioned before that I’m having trouble taking what is observed and extrapolating that into evolutionary theory. Not that I dismiss the entire theory, much of it makes sense. I want to also mention that I have appreciated your responses. I have not just rejected your opinions and have learned a lot from you. But I guess there’s not much point in discussing things we agree on, so I will bring up things I either don’t understand or don’t agree with.

Thanks and take care


This message is a reply to:
 Message 75 by RAZD, posted 01-22-2010 7:56 PM RAZD has acknowledged this reply

Replies to this message:
 Message 80 by Taq, posted 02-09-2010 3:00 PM herebedragons has not yet responded

  
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