Thursday, July 15, 2010

Evolution Dialogue

(I found this in my inbox.  The draft was originally saved in October, 2008!)

(Person 1)  So let me see if I've got this right.  Mutations are a good thing. 
(Person 2)  You're being too simple-minded.  Mutations can't be assigned a simple label like "good" or "bad."
(1) But mutations are at the heart of evolutionary progression, are they not?
(2) Of course.
(1) And "survival of the fittest" through natural selection is the Holy Grail of evolution, right?

(2) Aside from the religious overtones, yes.

(1) But what if the vehicle of evolution (mutations) are inherently disease-causing?
(2) What do you mean?

(1) What if two of the basic components of evolution are at odds with one another?  What if the "cure" is worse than the disease?

(2) Meaning...

(1) Well, typically evolution is explained as the process by which organisms gain new "gadgets" so useful that the "haves" live longer than the "have nots."

(2) Right... just make sure you don't trivialize Nature's workings.

(1) But what else is in evolution's cornucopia?  What, besides "new gadgets" does the mechanism of evolution -- mutations -- bestow?

A recent article in the journal Nature is entitled "A Bigger Picture: Beneath cancer's daunting complexity lies a simplicity that gives grounds for hope."  (Nature 2008, 455, 138).  It describes a picture that is emerging from intensive studies to profile the mutations involved in pancreatic cancer or glioblastoma multiforme.  What they're finding is that the DNA of cancerous cells often have multiple mutations.  For example, pancreatic tumor cells showed an average of 63 mutations each.
(2) What does this have to do with evolution?
(1) I'm getting there!  Since mutations can cause cancer, should cancer be thought of as a byproduct/side effect of evolution?
(2) Hmmm...
(1) I'm curious: what's the average ratio of favorable to neutral to deleterious mutations?  If neutral mutations predominate, then it will be most important to know what the ratio of favorable to deleterious mutations is. 

If deleterious mutations predominate, then an organism would probably survive longer if it remained in an unmutated state.

But how much prettier is the picture if the ratio leans toward the favorable side?  A single mutation could be enough to cause cancer in an organism, and hasten its death.  So even if the ratio leans toward the favorable side, as an organism's DNA undergoes mutations, it will have increased rates of cancer.  Doesn't this seem like a pretty poor lottery to buy a ticket for?
(2) I haven't seen any hard and fast numbers on that.  Besides, some of the favorable mutations could halt cancer.
(1) I haven't seen the hard numbers either.  I'm just thinking about the link between mutations and cancer, and pointing out that the very "mechanism" of evolution has a high likelihood of causing disease.  As you point out, there's every reason to believe that some favorable mutations can halt cancer.  But since mutations are happening randomly, how can anyone expect the specific, protective mutations to take place just in time to nip the cancerous mutation in the bud? 

Bear in mind that an organism can have a host of favorable mutations that does it a lot of good, but it only takes one deleterious mutation for the whole organism to cycle into cancer.

(2) You sound like an alarmist.

(1) I was just struck by the strangeness of it all.  Or maybe I should say absurdity.  The first time I felt like this was when a guest speaker talked about his work on amyloid.  He proposed that amyloid could have been the first biomolecule: the first molecule of living organisms.  I don't know much about amyloid, but evidently it can self-assemble into some pretty complex structures.  If that's all we knew about amyloid, it'd sound pretty sweet.  Step aside DNA, RNA, and protein!  Amyloid was really the first biomolecule!  Problem is, that isn't all we know about amyloid.  Amyloid plaques form in Alzheimer patients' brains.  Even though the entire cause/effect of amyloid/Alzheimer's isn't known, if there's any likelihood that amyloid is inherently disease-causing, isn't it ironic or even absurd to claim that it was the first biomolecule? 

Sometimes I feel like my brain is a sensor for absurd statements/claims.  I think that might be why I keep on spontaneously thinking of reasons why I have rejected evolution.

(2) Does your brain have trouble with the virgin birth?  Or the so-called "resurrection"?
(1) Those do sound absurd, don't they?  And they would be absurd, except that I'm not claiming that they happened by random chance.  I know that they happened by the direct intervention of an intelligent Being called God.

(2) There you go again.  As soon something happens that you can't explain, you revert to God.

(1) Well, when it comes to the virgin birth and the resurrection, be clear on what you're criticizing me on.  What do you believe about these events, and where do we differ?  There's three choices: A) the events never happened, so there's no need to explain how they happened, B) the events happened, but there's no explanation, or C) the events happened, and there is an explanation.  In what you just said, you seem to be implying that you believe choice (B).

(2) Okay, okay.  I don't think they happened, but you do, and you think God did them.  But those are "spiritual" things.  The things that God has (in His supposed wisdom) put outside the reach of science.  What about just material things, like the development of one organism from another?
(1) Neither of those events is purely spiritual.  When a virgin conceived a child, or when a dead man came back to life, the spiritual and the material dimensions were altered.  God demonstrated His mastery over both those arenas. 
What point of the miracle is most troubling to you?  Is it the claim that it happened at all, or the fact that God didn't give us the mechanism by which He did it?
Even though He didn't tell us the mechanism He used, the result of these miracles is not outside the realm of science.  The child that the virgin bore could be seen, felt, smelled, etc.  When the man that child became was crucified years later, he was measurably dead.  Those gathered at the cross heard Him breathe His last breath, and saw His body sag against the nails on the cross.  But impartial observers could give even more definite accounts of His death.  A man had to be certifiably dead before he could be removed from a cross, and which Roman soldier would be willing to risk his skin to let a live man descend from a cross?  If there was any doubt that Christ was dead, it was put to rest when a soldier plunged a spear into his side, and blood and water from Jesus' heart and pericardium ran out. 

So if Jesus really died, did He really ever live again?  Physical and spiritual change, with physical evidence to back up the existence of hte piriual change

(1) [1 mounts soap box] What drives chemical evolution forward?  I mean, what drives the evolution of non-living matter?  They don't really care about surviving, because they're not even alive!
Timing: at one of the crucial points in evolutionary history, millions of years had no bearing.  That point was when life came from non-life.  There's no magical substance that had to be there, to initiate the process.  It would need to occur countless times, and continue happening today.  There's no reason to belive that life developed spontaneously only once.  I do "evolutionary selections" in my research, and it's pretty common for a selection to result in nothing.  I'm looking for a DNAzyme that cleaves an RNA bond under certain conditions.  From talking to other folks in my lab who have done this longer than me, it's fairly common to need to do "reselections."  That makes sense: if the conditions in which you set up a reaction are too stringent, even if you're sampling a pretty sizable slice of sequence-space, there's always the chance that none of the DNA you're sampling has the activity you're looking for.  Maybe the concentration of Cd(II) you've included is too low, or maybe the time period you're allowing the reaction to proceed for is too ambitious.  Anyhow, you run your DNA pool on a gel and see that only uncleaved DNA is present. 
    To translate that to biological evolution, who's to say that the first round of selection is going to work?  Maybe the first organism that evolved died an hour after it evolved.  Then what?  Well, you simply run another non-life to life reaction!  So this reaction needs to be ongoing.
    It's like building a fire: the first one might go out, so you need a steady source of matches to make sure you can light another one.
    Of course, since supposedly nature isn't directed, life wouldn't be forming spontaneously from nonliving matter only when the previous batch of living organisms had died out.  It would be progressing whenever the required reagents and catalysts were assembled, and pressure and gaseous conditions were right.
    The reaction would then take off instanteously. 
    So I'm wondering, when did nature's spontaneous generation lab close, and why? 
    Is our only hope to simulate the conditions that gave rise to life in the past, since nature somehow inexplicably gave up on it herself?
    Given our ready access to Sigma-Aldrich, our incredible ability to introduce reagents and catalysts, and adjust pressure and gaseous conditions, why haven't we simulated this yet?  And, more importantly, why haven't we observed life arising from non-life in nature?
    Since no one has observed life arising from non-life, either in nature or in the lab, it cannot be the bedrock of any scientific theory. 

(2) You're too dogmatic.

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