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Author Topic:   Examples of new information
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 12 of 31 (656328)
03-17-2012 5:13 PM
Reply to: Message 9 by dan4reason
03-17-2012 4:20 PM


My issue with the example is that I want to make sure that adaptation actually came about by natural selection and mutations, not something else.
In many experiments, we can check this very easily. We can see that gene switching is not a possibility by looking at the actual DNA sequence and finding the mutation; and we can check that it is not a result of lateral gene transfer (of plasmids or anything else) by using a clonal line --- that is, you do the experiment starting with just one bacterium, yeast cell, or whatever.
In the case of the nylon-eating bacteria which Percy mentioned, the first condition holds but not the second, since this development occurred in nature and not in the laboratory. (However, one might in lieu of it consider the fact that prior to the invention of nylon, a nylon-eating bacterium would have starved to death, so common sense suggests that the development of the gene must involve a novel mutation.)
However, there are plenty of experiments where both conditions apply --- we can identify the mutation, and we can be certain that the founder of the population didn't have it. One example would be Lenski's experiment, which you may have read about.
Afterthought added by edit: another way we can rule out gene switching is if we can watch the process of change and know that it didn't happen immediately. If it was a pre-programmed response to environmental factors, then it would take place on introduction to the organism into the new environment, whereas if the change is a result of genuine evolution this will hardly ever be the case. So it is not always necessary to look at the gene directly.
For example, when we watch the evolution of multicellularity in chlorella, not only does it not happen instantly, but we can observe several steps in the process as the first crude mutation is progressively refined to the optimal form. If this change was pre-programmed, then we'd see every organism in the experiment switch to the optimal form within the first generation, would we not? If it looks like evolution and quacks like evolution, it's probably evolution.
Edited by Dr Adequate, : No reason given.

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 Message 21 by dan4reason, posted 03-18-2012 2:45 PM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 15 of 31 (656338)
03-17-2012 6:51 PM
Reply to: Message 14 by Trixie
03-17-2012 6:31 PM


Re: HIV-1 Vpu
I love the last comment on that page. You could show it to kids and explain that this is why they shouldn't get into ID --- "this is your brain, and this is your brain on creationism ..."

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 17 of 31 (656364)
03-17-2012 11:22 PM
Reply to: Message 16 by Nuggin
03-17-2012 7:31 PM


As I read your question, you seem to be asking for the development of a new gene, but one which does not in turn require the loss of another gene.
What he means by gene switching is, well, gene switching. That is, he very reasonably wants assurance that the novel characteristics of the organism are not caused by the switching on and off of pre-existing genes as a pre-programmed response to a novel environment. Your example is therefore unnecessarily complicated (besides being hypothetical).

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Replies to this message:
 Message 18 by Nuggin, posted 03-18-2012 1:44 AM Dr Adequate has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 19 of 31 (656372)
03-18-2012 1:57 AM
Reply to: Message 18 by Nuggin
03-18-2012 1:44 AM


Re: Pointless question then...
Well, yes, we do seem to be done apart from the bit where d4r says "thank you".
Edited because d4r isn't a creationist, he's just talking like one for no apparent reason.
Edited by Dr Adequate, : No reason given.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(3)
Message 24 of 31 (656461)
03-18-2012 10:07 PM
Reply to: Message 21 by dan4reason
03-18-2012 2:45 PM


That seems reasonable, however we need to be sure that the mutation is actually in a gene that codes a protein.
I could not find any info on the specific mutation that allowed these bacteria to digest citrate. How do you know it was not a mutation to a gene controller?
Well, if you look at the DNA directly you can see where the mutation is and so what it's affecting, whether it's in protein-coding DNA or something else.
I'm not sure why you think it matters, can you expound on this?
How do you know that the enzyme that nylon eating bacterium used to break down nylon wasn't formerly used for something else?
Well, there aren't bacteria using it for something else.
That seems reasonable but it doesn't rule out gene switching.
Well, yes it does. Why do you think it doesn't?
If gene X is switched on as a consequence of environmental stimulus Y, then you'd see the whole bacterial culture switching on gene X in the first generation exposed to stimulus Y.
You mention how a crude mutation is modified to produce multicellular. This example seems like the silver bullet I am looking for. What type of genes were these mutations happening in?
Genes controlling cell division, natch. I can't find the full text of the relevant articles, just abstracts, but I don't think the researchers did look at the DNA, that's why I gave it as an example of something that one could deduce wasn't gene switching by other means.
The original experiment was done, so to speak, by accident. Dinoflagellates (single-celled predators) got into a culture of chlorella (single-celled prey), which was not what the experimenters wanted to happen. It was lucky for them they didn't just throw it out, but investigated what was going on.
One way chlorella can avoid predation is simply to get too big for the dinoflagellates to eat, and this is what happened.
Now, my reasons for thinking that this wasn't gene switching are as follows:
* The change was not immediate and universal.
* The first change was that cell division was interfered with to such an extent that big blobs of as many of a hundred cells were formed. This has the advantage that the chlorella couldn't be eaten; it has the disadvantage (one presumes) that the cells on the inside would find it difficult to acquire nutrients. The chlorella then tended towards an eight-celled form which was still too big to eat but in which every cell was on the outside of the cluster. Wouldn't gene switching jump to this form immediately?
* This never happens in the wild. Why not? Because in the wild chlorella is not just preyed upon by single-celled predators such as dinoflagellates. A clump of chlorella is too big for a dinofalgellate, it's a tasty meal for a fish. Why would chlorella have a genetic switch just to cope with conditions only met with in the laboratory?
* When the eight-celled forms were transferred to an environment without dinoflagellates, their descendants continued to have the eigth-celled form. Now, this would be something unique in gene switching --- a gene which can be turned on, but can't then be turned off, and is inherited stuck in the on position.
So I think this is a good example of what I'm talking about --- in this case, even if we don't directly look at the DNA, it seems safe to conclude that we're looking at the results of mutation.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 28 of 31 (656915)
03-23-2012 3:26 AM
Reply to: Message 27 by pandion
03-23-2012 2:51 AM


Re: biological information is simple
The requirement for a new function is a boondoggle.
I think it's the other way round.
The acquisition of new functions is precisely what adaptive evolution is all about, and asking to see it happening (in appropriately small quantities) is a perfectly legitimate request. Dragging the language of information theory into the discussion is the boondoggle, unless at some point creationists propose to do any actual math with it.
Edited by Dr Adequate, : No reason given.

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