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Anthony Horvath

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Evolution by Faith
« Reply #40 on: June 13, 2006, 08:04:58 PM »

"Heh. William Purves book is an intro-level biology text written for High School students."

So sorry, Broken.

UCLA uses it:
http://www.lscore.ucla.edu/ls1.html

Its used at Reed College:
http://academic.reed.edu/biology/courses/BIO263/

Here it is at a British college:
http://lib5.leeds.ac.uk/rlists/biology/blgy1211.htm

And here it is at flippin A God Almighty Yale:
CLICK HERE

That's the google cache.  It seems they have restructured their site.  I couldn't find a link for course home pages to see if they still use the book or not.  That link is for summer of 2005.  at YALE.  Sometimes its embarrasing to see how far people will go to try to marginalize others.

"SJ, I have given you pages of biological phenomena which don't make sense except in terms of evolution."

No, you absolutely have not.  Transposable elements make sence in terms of GENETICS.

"In fact, I have repeated many examples over and over again."

As this is the first time that I am aware of that we have that we have directly addressed this particular issue, this comment is hogwash.

"Does the mitochondria example ring a bell? The fact that the mitochondria in our cells reproduce like bacteria, have bacterial genomes, bacterial ribosomes, and have gene sequences closely related to certain invasive bacteria which they physically resemble is difficult to explain except by evolution. You certainly have never provided a Creationist explanation."

You do not need either evolution or creationism to understand these things.  Let's look at this paragraph in more detail:

"Does the mitochondria example ring a bell? The fact that the mitochondria in our cells reproduce like bacteria, have bacterial genomes, bacterial ribosomes, and have gene sequences closely related to certain invasive bacteria which they physically resemble is difficult to explain except by evolution. You certainly have never provided a Creationist explanation."

You don't need an 'explanation' to understand what is being observed.  In your paragraph you resorted completely to genetics.   We have different notions at work here.  You think you've done something impressive if you've 'explained how.'  That's why you think I need to offer a 'creationist explanation.'  This is far from the point.  The only reason anything needs to be explained in the first place is because the genetics are known in the first place.  You don't need to have a theory on 'how' the mitochondria got here in order to understand the genetics of how it is.

Certainly, except for 'mitonchondrial eve' type theories which seek to expand on this alleged 'how,' I doubt you could provide me any meaningful examples why thinking of the mitochondria in evolutionary terms, rather than genetic terms, is the key to understanding the mitochondria.

Go ahead, give it a shot.  Pick any biological feature that you want and try to explain to me how it only makes sense in light of evolution, without referencing genetics.

"Or how about the broken vitamin C gene in apes and humans? The exact same gene broken in exactly the same way in exactly the same spot. How do you explain it except by common ancestors?"

Genetics.  Without genetics, you wouldn't even know that anything was the 'same.'   Don't you see where the problem is in your whole approach?  

"Also in ape and human genomes, virus genomes inserted in exactly the same spots in our DNA. Also, the amalyse gene with a retrotransposon inserted in the very same spot in the genomes of all old world monkeys, including us. How do you explain these phenomena except by common ancestry?"

Man, that's an awful lot of genetics in there.  Why should it need an 'explanation' ?   You can know all the things you said above without having any need to invoke an explanation.  They are simply brute facts that you can observe.  You gain nothing by drawing an inference about the source or origin that cannot be gained by simply sticking to straight genetics.

"There are endless other genetic examples,"

"I look forward to your usual dodging, followed by your usual mental deletion or denial of all information contradicting your view of reality."

There is no dodging.  My argument is plain:  you cannot understand biology without genetics.  You can understand it without evolution.  Evolutionary theory moved to accept Mendel.  Mendel did not move to accept evolutionary theory.

I am now on my second reading of this college text book.  It begins with genetics and doesn't stop with genetics until about page 425.  It would seem as though genetics is an important part of biology.  :)  Finally, after 400 pages of discussion about genetics, it finally gets to evolution.  The really funny thing is that in this book allegedly on biology, the arguments it draws on for that part are based on geology, not biology.  Too funny.   Then, beginning on page 450 (The Mechanisms of Evolution) it is back to genetics until page 500.

No, the proof is in the pudding.  In order to understand biology, you need to know genetics.  Do you deny?
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« Reply #41 on: June 13, 2006, 11:25:58 PM »

Quote from: sntjohnny
"Oh, let's not go over that many-times-refuted argument again. You know from previous exchanges that such periods are easily explained as post-extinction periods when biological diversity explodes to fill ecological niches. Such periods were not inconsistent with Darwin, and he even anticipated them. Argumentum ad nauseam."

Thanks for making my point.  ;)  Everything is consistent with Darwinism.  
That's the point.

My point was that only your claim about punctuated equilibria was easily explained within the Darwinian paradigm.  That is in no way equivalent to saying that EVERYTHING is consistent with Darwinism.  

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"I doubt that you would qualify as a cognitive scientist,"

Well, I personally wouldn't assert it for myself, but don't you think its a little funny how the credentials of others 'don't matter' to you only when they agree with you?   For example, as applied to yourself?   You are not a geologist, a biologist, a physicist, but you still think you are perfectly competent to hold forth on all sorts of topics.


Utter nonsense.  I have never said or implied any such thing.  In fact, you were the one to introduce the topic of "credentials" here.  Apparently, you really, really want me to make an appeal to authority argument.  So you keep reconstructing that straw man and knocking it down.

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You can continue to try to frame the argument in terms of ridiculing the position because of the credentials or lack thereof of the person, suggesting that they 'don't understand,' but the more objective reader will detect that what's really going on is not a lack of understanding, but a simple matter of disagreement...


We are in violent agreement on that point, at least.  :-)  You and I disagree on the nature of science, and one doesn't have to be an expert to understand that disagreement and form an opinion.  I have not attacked your credentials as a scientist or event tried to advance my own as a cognitive scientist.  Again, this whole issue seems to be entirely of your own construction.  It has nothing to do with my criticism of your position.

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"As I've said before, this is about what science is, not who has credentials as a scientist."

But that is not in fact your real position.  Your idea is that you are able to say what science is but the rest of us can't.  Unless we agreed with you.  Then we can.


Amazing.  I point out that credentials are not the issue.  You tell me that this is not really my position, presumably because you can read my mind and know exactly what I am thinking.  Having arrived at the conclusion that I believe the exact opposite of what I said, you then criticize me for not agreeing with what I said.  

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Now, the funny thing is, I've said repeatedly that I don't give a pile of dung about what anyone thinks about 'science.'  


I do think it a bit odd that you keep repeating what everyone already knows.  Do you think that we are not aware of this?  You seem proud of your disdain for what others might think about science.  I'm not sure why, but what the heck.  You are entitled to your opinion, and others are entitled to disagree with it.

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Unlike atheists, I understand that groups are allowed to define themselves.  Atheists, of course, presume to define Christians and all their terms, and know more about their positions, etc, etc.  That's not the way I operate.  I think Christians should have latitude to define the things they are most familiar with for themselves, and then you can react to that.  Since that is true, I naturally should extend the same courtesy to the scientists. If scientists wish to define science in a certain way, I hardly care.  I distinguish my own view from theirs in order to make plain my point.


I'm going to go out on a limb here and say that you are trying very hard to let scientists themselves define what science is, since you believe that Christians have the right to define Christianity.  You think it's ok to define science differently from the way scientists do, but you criticize atheists in general for trying to redefine Christianity on their own authority.  Is that a good synopsis of what you're trying to say?  It all seems confused and contradictory to me, but I can't really think of any other good way to paraphrase your argument.  Perhaps you could make it a little clearer.

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I call myself an experimentalist for a reason.  That reason is that there are clearly differences in epistemological value for different sorts of methods for inquiry.  My aim is to make it clear which sorts of methods I consider of value in what contexts.  I don't really care if others don't want to engage in that manner of critical thinking.


OK, as long as you don't give the false impression that scientists have ever construed their own endeavor in the same narrow terms that you do.  Science attempts to understand observations about nature, and not all scientific theories are equally amenable to laboratory experiments.  Calling yourself an "experimentalist" strikes me as a bit strange, because you have never really conducted scientific experiments yourself, have you?  You just mean that you hold an epistemological position on the nature of what scientists do.  You choose to discount scientific theories that merely attempt to account for observable phenomena without the benefit of lab experiments to back them up.

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But I do care that you sweep my distinction aside altogether so as to make it sound like I'm attacking 'science.'


In the sense that you are redefining science so as to exclude much of what scientists do, I think that you are attacking science.  However, you seem to also acknowledge that scientists are allowed to disagree with you.

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"What is your point in going on about this? Are you trying to say that your anecdotal survey was scientific?"

Uh, no.  But your objections were that it was flawed.  Flawed how?  Flawed from a scientific POV.  How can it be flawed from an anecdotal POV?  Did I ever offer it as anything more?  You have conceded the point that that anecdotal survey was meant to convey, so its not worth dwelling on.


Let me clarify.  I do not consider it flawed as a subjective opinion that incorrectly confuses the goals of applied and theoretical science.  That's exactly what it is.  I think I've made my point clear, and I'm happy to move on.

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"I don't see the point of this line of argument."

Of course you don't.  I wouldn't expect you to.


What a relief.

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"Evolution informs scientists about every aspect of biological organisms, not just the Golgi complex. Why are you fixated on that?"

I'm not fixated on it at all.  I have 100 more examples ready to go.  You want to have your cake and eat it, too.  You want to insist that evolution informs scientists- I believe we were talking about doctors, though, right?  people who really depend on the stuff- about biology.  Well, the GA was just one example.  I'm giving you an opportunity to show how evolution informs the biological understanding of GA.   You seem to be unable to do this, or unwilling.  My google search showed only 3 hits (and they weren't very good) suggesting any kind of way that evolutionary theory adds to our understanding of the GA.


I've already pointed out that doctors, who are applied scientists, have little direct need to apply evolution theory to their everyday practice.  So, I don't see why we need to talk about doctors at this point, and you haven't responded to my attempts to get clarification.  I believe that we've both established that evolutionary theory has been used to explain the origin of the Golgi complex, and the web sites you found seem to support that claim.  Maybe you can help the process by explaining what you are hoping to show by this line of argument.

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What if I go through 100 aspects from biology without you being able to provide a single instance where evolution informs it in real life application in any meaningful way?  For that matter, in most cases, it doesn't even inform the theoretical.  It certainly did not for the GA.  How many examples do I need to produce before you concede that perhaps evolution isn't really as necessary to understand biology as you think?  1,000?


You might be able to give me a thousand examples of physical phenomena that don't require general relativity to explain, but that doesn't mean that we should abandon the theory of general relativity.  You don't seem to be on the verge of constructing a logical argument here, so again I ask for clarification.  What are you hoping to prove from this line of argument?  That if some things can be explained without direct appeal to evolution, then we can comfortably abandon the theoretical cornerstone of biology?

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I am confident that I could very easily produce 10,000 examples.  Easily, but it would take some time, but easy.


10,000 examples in support of a flawed argument are no better than one.

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"Is this something that is a theme in creationist attacks on evolution theory?"

I wouldn't know.  I don't read creationist literature.


Then there may be hope for you yet.

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"I'm not sure why you are pursuing this issue."

Hopefully you understand a bit better now.


Not really.  Your argument seems to lack validity, as far as I can see.  Sorry.

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"Apparently, you have forgotten that there is a big difference between theoretical and applied science."

Not at all.  There certainly is a direct connection between many aspects of research science and applied science.  Just not evolutionary research.


Why do you think that doctors should need to make direct appeals to evolution theory in their daily work?  What better scientific theory would explain that alleged phenomena better?  What is the point that you are trying to make here?

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Every piece of biological data that I've come across can EASILY be understood outside the context of evolutionary theory.  So easily, in fact, that people who really spend time applying biological facts in real life and death contexts can completely ignore it.  A 'metaphysical research programme' if you will.  ;)


I would only point out that you have had a rather limited exposure to biological data compared to actual biologists, so I'm not surprised that you find evolution theory unhelpful in your world.  It all depends on what you think needs explaining.  The nature of scientific theories is that they usually define the nature of what counts as data.  So laymen very often don't even know what questions to ask.  If you don't know what a phoneme is, then you wouldn't consider rhyme or alphabetical systems to constitute evidence for phonemes.  Linguists, on the other hand, do see rhyme and alphabets as data to be explained by theory.  (Well, some of us do, anyway.  :-))

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The only place where I've seen applied scientists actually appeal to evolutionary theory in any respect is ecology.  And even that is usually of the 'be sure to take your full course of anti-biotics' stuff.


Actually, that's what doctors tell you, not ecologists.  ;-)  We know that bacteria will evolve to render antibiotics ineffective if people stop taking them before all of the bad bugs have been eliminated.  That's because the stronger bugs then multiply to fill in the ecological niche.

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Or, to put it back into the context of the thread, even the medical community is asked to take evolution on faith.  It informs practically nothing that they do.  Oh yea, except for the antibiotics.  Don't forget the antibiotics.


Yeah, and just about everyone else who is interested in biology,  including biologists, archeologists, geologists, and so on.
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Anthony Horvath

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« Reply #42 on: June 14, 2006, 01:26:05 AM »

"That is in no way equivalent to saying that EVERYTHING is consistent with Darwinism."

Sure, but it shows how in this one particular example how mutually exclusive observations can be shown to be 'easily' consistent with Darwinism.  If this were the only example, I'd cut it some slack.  But particular examples of the same sort of thing multiply quickly.  Many of them can be pieced together on this forum alone.

"In fact, you were the one to introduce the topic of "credentials" here."

Then I'll hold you to it.  Maybe you could put some smack down on Cogito.  This is explicitly his point on this matter.  It was your point on the anthropomorphism thread.  

"but a simple matter of disagreement..."

"We are in violent agreement on that point, at least.  You and I disagree on the nature of science,"

Cop.  I am completely perplexed.  A great deal of the rest of your thread follows from this, and its just rubbish.  How can you say that we disagree 'on the nature of science' when I have been completely clear on the nature of my argument?  Not just here, but elsewhere, too?  Let's just briefly touch on one statement:

""Now, the funny thing is, I've said repeatedly that I don't give a pile of dung about what anyone thinks about 'science.'"

To which you replied, in part,

"You seem proud of your disdain for what others might think about science. I'm not sure why, but what the heck. You are entitled to your opinion, and others are entitled to disagree with it."

You are clearly interpreting this statement of mine as an attack on science.  But this, connected with my next statement makes it perfectly clear that the point of my argument has nothing to do with science, or its nature.  I mean, I really don't care.  Scientists can define science however they want.  Words mean what we agree that they mean.  Leaving aside areas where I think they completely overstep, the fact remains that I am perfectly willing to allow 'scientists' or their apologists (that would be you) to presume that philosophical naturalism is an explicit part of whatever else will make a method 'scientific.'  Go for it.  Whoopteedo.  However, that being said, the mere fact that you can explain data within a construct that rules out supernatural agency a priori doesn't mean that much to me, either.

Thus my insistent and persistent statements to the effect that I choose to define myself as an experimentalist.  More below.

"I'm going to go out on a limb here and say that you are trying very hard to let scientists themselves define what science is, since you believe that Christians have the right to define Christianity."

Any group has permission to make their own definitions, right.  Different definitions can be allowed in contexts of debates like ours provided there is mutual agreement.

"You think it's ok to define science differently from the way scientists do,"

ARARRALGAGGHDGHDGHDSKGJ   That is to say, no.  I have no interest in speaking to the topic of 'science' at all.  It is irrelevant.   Insofar as I am willing to grant validity of certain findings within science, I am only willing to do so if they are experimentally generated with little to no philosophical insinuations.

"It all seems confused and contradictory to me, but I can't really think of any other good way to paraphrase your argument. Perhaps you could make it a little clearer."

Well, perhaps it wasn't helped by my cheap shot at atheists for insisting that they can tell Christians about Christianity.  Recall your statement that you think a Christian can believe that Jesus is not God.

Emphatically, my own position is that I am an experimentalist.  If science is not constrained to experimentation, that is not my problem.   That is not to say it does not make wide use of experimentation, but it certainly is not constrained to it by any measure.

Thus, you can continue to churn out scientific 'facts' all day long, but if these 'facts' primarily derive from an a priori preclusion of supernatural explanations,  and not necessarily from direct experimenation to boot, I do not feel compelled in the slightest to think these facts are TRUE.

I have made this point so constantly and consistently that I am astounded that you are confused by it.

"OK, as long as you don't give the false impression that scientists have ever construed their own endeavor in the same narrow terms that you do."

Pasteur did.  Newton did.  Mendel did.  Sure- Dawkins doesn't.  Gould didn't.  Sagan didn't.  Right.

"Science attempts to understand observations about nature, and not all scientific theories are equally amenable to laboratory experiments."

Well, that is certainly true, isn't it?  lol  That's pretty much the point.  Do you deny that there is not an epistemological difference between something that is directly observed as opposed to something that is inferred, instead?  The inference may be reasonabe:  assume it is for the purposes of this question.  Is it really your position that the two are of the same epistemological value?

"Calling yourself an "experimentalist" strikes me as a bit strange, because you have never really conducted scientific experiments yourself, have you?"

I'm not really sure what you mean by this.  Haven't we all conducted SOME scientific experiments, even if they were only in high school physics class?  I know I did.  I presume instead you mean that I haven't conducted the empirical (I'd rather not use the word 'science' because that is question-smuggling) experiments for a great many things considered to be reliable facts of nature.  Obviously I haven't.  But neither have you.  More in a moment.

"You choose to discount scientific theories that merely attempt to account for observable phenomena without the benefit of lab experiments to back them up."

Discount?  Discount, no.  Do I recognize that there is an epistemological difference?  You bet I do.  But I do something else.  I also know that I am not able to participate in a great deal of the experiments that I should like to do, and I'm sure this is true for you, too.  Furthermore, aside from hoping to recreate the experimental results themselves in a separate experiment of our own, we will be unable to reproduce the experiments in the past, too.   Thus, even though it is not explicitly treated by most, it is something that I specifically take into consideration.  Why should I believe that these past results were honestly conveyed to us?  Take the Michelson-Morely experiment as an example  I can't reproduce the experiment.  I apply historical methods to detect the nature of their testimony about the facts they allege, and testimony verification techniques to evaluate whether or not I can reliably trust their testimony, once I've established what it is.

Michelson-Morely do not get a pass from me just because.  

Similarly, scientists today don't get a pass, either.  If I cannot re-create their experiments, what am I to do?  I am not powerless.  Do they have an agenda?  Do they have a bias?  Do they have philosophical pre-suppositions?  How much of their experimental conclusions interacted with this philosophical material?  Did they take steps to winnow out such things?  It is helpful if other scientists corroborate the experiment- but if they share the same dispositions I may have reason to remain skeptical.

The primary assumption sitting underneath science today- especially present in evolutionary science- is that the data absolutely must be interpreted in a naturalistic framework.  It does not surprise me, therefore, when scientists are able to interpret their data in a naturalistic framework!  But what if the whole question was whether or not this assumption is really reasonable and rational?  You cannot prove it is reasonable and rational while simultaneously assuming it.

The theory of evolution forbids itself from considering non-agency interpretations of the data.  To the extent that scientists think they are doing a great job of continuing to interpret the data in light of that preclusion, I commend them.  Human imagination knows no limits.  Is it 'scientific'?  I hardly care.  Is it true?  THAT I care about.  And I don't happen to give much weight to claims that rule out certain interpretations out of hand, regardless of whether or not some think that is essential to their methodology.

"I've already pointed out that doctors, who are applied scientists, have little direct need to apply evolution theory to their everyday practice."

:)

"I believe that we've both established that evolutionary theory has been used to explain the origin of the Golgi complex, and the web sites you found seem to support that claim."

lol, the 3 web sites?  On the one hand, no, I do not agree that the GA has been explained by the TOE.  Clearly scientists think that it can be.  But there is a chasm between 'can be' and 'is.'

"Maybe you can help the process by explaining what you are hoping to show by this line of argument."

Quite simply:  Genetics forms the basis for understanding biology, not evolution.

Genetics is all about experimentation, baby.

"What are you hoping to prove from this line of argument? That if some things can be explained without direct appeal to evolution, then we can comfortably abandon the theoretical cornerstone of biology?"

lol.  2 things.  First thing.  You are making an equivocation that I am not.  Broken did the same thing.  There is a difference between 'explain' and 'understand.'  You can understand the GA completely independantly from how one explains its origins.  Second thing:  if ALL things can be understood without direct appeal (and almost certainly without indirect appeal in many cases) to the theory of evolution, then on what grounds can it really be said that evolution is the 'theoretical cornerstone of biology' ?  If it never has to interact, why think it ever does or should?

This goes to the heart of the epistemological differences involved in these matters.  The biochemical nature of the GA, and how it operates within the cell, what it accomplishes, the diseases that occur when it doesn't work correctly, etc, can all be understood without any kind of reference to either evolution or creation.  The so called 'explanation' is irrelevant to what is directly observed.  The 'explanation' is untethered from the direct experimentation.

At best, in this example, any particular explanation is merely inferred.  Perhaps it is the right inference- nontheless it is an inference, and is of a different epistemological value than what can be gained by direct observation.  And if that inference is predicated on the notion that one must seek a non-agency explanation, I certainly don't feel like I need to consider it very reliably established that the data actually suggests that a non-agency explanation is demonstrated.

Not only that, but I can go about my life.. if I were a doctor, a biochemist, a pharmacist, whatever... completely competent on the understanding based on the actual observations without even a glance at any alleged 'explanations.'

Thus, I suggest that if the TOE has no significant practical applications, perhaps it is not even a very good 'metaphysical research program.'  Perhaps it only exists for one reason and one reason only- and that reason philosophical, not empirical.

"I would only point out that you have had a rather limited exposure to biological data compared to actual biologists, so I'm not surprised that you find evolution theory unhelpful in your world."

That is why I mentioned the people that I did.  Apparently quite a few actual biologists find it unhelpful, too.  Did you fail to note my reference to the biochemist who worked at a major drug company?  Evolutionary theory was completely irrelevant.

"It all depends on what you think needs explaining."

Bingo.  But experimentally speaking, not everything can be explained.  That doesn't mean you get to make up explanations based on your presuppositions.  If the experimental data is limited- that's life.  Deal with it.

"Actually, that's what doctors tell you, not ecologists."

I was speaking of the category of 'evolution' that the ecologists I've read will cite.  Microevolution may be the mechanism that ya'll think justify macroevolution, but it nonetheless remains that you can dismiss macroevolutionary 'explanations' altogether and still function just fine.
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« Reply #43 on: June 14, 2006, 03:09:29 PM »

Quote from: sntjohnny
"Heh. William Purves book is an intro-level biology text written for High School students."

So sorry, Broken.

UCLA uses it:
http://www.lscore.ucla.edu/ls1.html

Its used at Reed College:
http://academic.reed.edu/biology/courses/BIO263/

Here it is at a British college:
http://lib5.leeds.ac.uk/rlists/biology/blgy1211.htm

And here it is at flippin A God Almighty Yale:
CLICK HERE

That's the google cache.  It seems they have restructured their site.  I couldn't find a link for course home pages to see if they still use the book or not.  That link is for summer of 2005.  at YALE.  Sometimes its embarrasing to see how far people will go to try to marginalize others.


From the Amazon review of Purves's book:

"His clear explanation of the concepts with bright, colorful pictures have helped my students to understand biological concepts for the AP Bio exam as well as preparing them for college."

Whether used as a high school or freshman college text, we are still talking very intro-level biology. Molecular Biology majors will typically take many additional courses in molecular biology, eukaryote and prokaryote cell biology, biochemistry, molecular genetics, immunology, and virology. And that is just at the undergraduate level.

So, to claim that the lack of detail on transposable elements (TEs) in a basic book like Purves somehow makes the subject of TEs unimportant is just silly.

TEs are highly interwoven into our genomes and, in fact, represent over 40% of our total DNA. These parasites are rapid mutators, integrate themselves into the genes of all plants and animals, and are a major evolutionary force.

Viral and plasmid TEs are also responsible for transmitting genetic material between unrelated species. In the book by Fred Bushman I mentioned earlier, Lateral DNA Transfer, (Amazon LINK), his lead-off example is rather astonishing (from a reviewer):

One example of lateral DNA transfer concerns marine bacteriophages in the oceans. Each milliliter contains on the order of ten million viruses, most of these being bacteriophages, which infect bateria. When these phages grow, some of them pick up the genes of the host cell and transfer them via infection to a new cell. The transferred sequence then can become stable, and from experiments this happens one out of 100,000,000 times. Due to the vast size of the oceans, this translates into 2 million billion lateral DNA transfers per second!

Rather thought provoking, to think of the ocean as a gigantic genetic super-computer. Makes you wonder what genetic program is running out there, doesn't it?
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You do not need either evolution or creationism to understand these things.  Let's look at this paragraph in more detail:

"Does the mitochondria example ring a bell? The fact that the mitochondria in our cells reproduce like bacteria, have bacterial genomes, bacterial ribosomes, and have gene sequences closely related to certain invasive bacteria which they physically resemble is difficult to explain except by evolution. You certainly have never provided a Creationist explanation."

You don't need an 'explanation' to understand what is being observed.  In your paragraph you resorted completely to genetics.   We have different notions at work here.  You think you've done something impressive if you've 'explained how.'  That's why you think I need to offer a 'creationist explanation.'  This is far from the point.  The only reason anything needs to be explained in the first place is because the genetics are known in the first place.  You don't need to have a theory on 'how' the mitochondria got here in order to understand the genetics of how it is.


Sorry, but if your theory cannot account for known facts, it is not a valid theory of science. At least give it a shot.

Here, I'll help you: maybe the "Creator" just got tired of building life from scratch. So He scooped up some rickettsia bacteria, tinkered a little bit, stuffed them into our cells, and presto-chango, instant mitochondria! OK, not very plausible compared to the evolutionary explanation, but at least I tried.
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Certainly, except for 'mitonchondrial eve' type theories which seek to expand on this alleged 'how,' I doubt you could provide me any meaningful examples why thinking of the mitochondria in evolutionary terms, rather than genetic terms, is the key to understanding the mitochondria.

Don't confuse "mitochondrial Eve" genetic tracing with the symbiogenesis of mitochondria. Entirely different subjects.

Don't confuse yourself by thinking evolution and genetics are somehow separate subjects. They are joined at the hip, especially at the molecular level. You can't understand genomes without evolution and you can't understand evolution without understanding genome dynamics.

You ask why thinking of mitochondria in evolutionary terms is useful. Simple. The closest relative to mitochondria are rickettsia bacteria, a gram-negative obligate parasite which lives inside eukaryotic cells (just like mitochondria do). The main difference is that the mitochondria's genome has atrophied down to just those genes the host eukaryote cell can't provide. So, if you want to understand why mitochondria are structured the way they are, study rickettsia. Pretty useful, no?

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"Or how about the broken vitamin C gene in apes and humans? The exact same gene broken in exactly the same way in exactly the same spot. How do you explain it except by common ancestors?"

Genetics.  Without genetics, you wouldn't even know that anything was the 'same.'   Don't you see where the problem is in your whole approach?  

"Also in ape and human genomes, virus genomes inserted in exactly the same spots in our DNA. Also, the amalyse gene with a retrotransposon inserted in the very same spot in the genomes of all old world monkeys, including us. How do you explain these phenomena except by common ancestry?"

Man, that's an awful lot of genetics in there.  Why should it need an 'explanation' ?   You can know all the things you said above without having any need to invoke an explanation.  They are simply brute facts that you can observe.  You gain nothing by drawing an inference about the source or origin that cannot be gained by simply sticking to straight genetics.


Lame. The conclusion of molecular genetics is that the only plausible explanation to the "matching mutations" puzzle is that humans and apes had common ancestors. Here's why:

From the genetic analysis, humans and apes have many of the same mutations. Some are negative in effect, such as the identical vitamin C gene mutation. Some are positive, as with the TE inserted into the amalyse gene. However, the probability of human and ape genomes having multiple mutations of exactly matching types, in exactly the same genetic locations is about the same as you winning the lotto three times in a row. In other words, zip.

So how did these identical mutations come about? The only answer compatible with molecular genetics is that apes and humans share a common ancestor who already had these mutations in their genomes. If you can find a molecular geneticist who disagrees, let me know.

So, your feeble dodge aside, the actual genetics answer to the "matching mutations" puzzle is common ancestry. I am still waiting for your Creationist answer. By the way, here is a Creationist making an honest  attempt to answer the very same question: LINK. Perhaps he can help you.

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"I look forward to your usual dodging, followed by your usual mental deletion or denial of all information contradicting your view of reality."

There is no dodging.  My argument is plain:  you cannot understand biology without genetics.  You can understand it without evolution.  Evolutionary theory moved to accept Mendel.  Mendel did not move to accept evolutionary theory.

Simply waving the word "genetics" around is not an answer to the "matching mutations" puzzle. It is just another dodge. The Creationist I linked to above made SOME attempt to provide a creationist answer.

By the way, genetics science has moved light years beyond Mendel, even light years beyond Watson & Crick. Evolution is essential to molecular genetics. Genetic recombination is a reality, whether by hybridization, transposable elements, or lateral DNA transfer. Genes are built from these evolutionary mechanisms. This is directly observable, in the laboratory.
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I am now on my second reading of this college text book.  It begins with genetics and doesn't stop with genetics until about page 425.  It would seem as though genetics is an important part of biology.  :)  Finally, after 400 pages of discussion about genetics, it finally gets to evolution.  The really funny thing is that in this book allegedly on biology, the arguments it draws on for that part are based on geology, not biology.  Too funny.   Then, beginning on page 450 (The Mechanisms of Evolution) it is back to genetics until page 500.


It is good that you are educating yourself. I am sorry your text has so little on evolution. Instead of re-reading Purves, try Campbell and Reese, which is the dominant first text for biology majors, with a heavy emphasis on evolution. Then move on to Bruce Alberts, "Molecular Biology of the Cell".
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Evolution by Faith
« Reply #44 on: June 14, 2006, 03:14:56 PM »

Quote from: sntjohnny
"It all seems confused and contradictory to me, but I can't really think of any other good way to paraphrase your argument. Perhaps you could make it a little clearer."

Well, perhaps it wasn't helped by my cheap shot at atheists for insisting that they can tell Christians about Christianity.  Recall your statement that you think a Christian can believe that Jesus is not God.


I was thinking of Arianism, which is now considered heresy by most christians, since it denied that Christ's divinity was the same as God's.  The loosest definition of a christian is just one who considers oneself a follower of Christ, not necessarily someone who believes that Christ was divine.  Most people tend to hold a narrower definition, and Christians quite often debate whether some self-styled christians really are christians.  For example, there is some confusion over whether Moromons should be considered christians.  Nobody and no group really has the authority to dictate what constitutes bona fide christianity, so I, a person who has no doctrinal axes to grind, tend to have a much broader definition than most christians.

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Emphatically, my own position is that I am an experimentalist.  If science is not constrained to experimentation, that is not my problem.   That is not to say it does not make wide use of experimentation, but it certainly is not constrained to it by any measure.


I understand your position, but I consider it somewhat arbitrary.  All you have appeared to mean by it is that you wish to drive a wedge between scientists that use controlled lab experiments to validate theories and those that rely on verifiable observations of natural phenomena.  That is, your use of this term 'experimentalist' has shown up in the past mainly in connection with denying that evolution has scientific validity.  Outside of that context, your usage seems to have no significance.

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Thus, you can continue to churn out scientific 'facts' all day long, but if these 'facts' primarily derive from an a priori preclusion of supernatural explanations,  and not necessarily from direct experimenation to boot, I do not feel compelled in the slightest to think these facts are TRUE.


That's your prerogative.  A scientific 'fact' is merely a theoretical consensus--one that scientists consider unlikely ever to be disconfirmed by observational data.  Evolution, in that sense, is a scientific fact.  If you choose to dismiss the scientific consensus, that's of little consequence to the rest of us.  If you want to promote your dismissal as reasonable, then you'll need to support it with something more than shoulder-shrugging dismissals of the findings of science.

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"OK, as long as you don't give the false impression that scientists have ever construed their own endeavor in the same narrow terms that you do."

Pasteur did.  Newton did.  Mendel did.  Sure- Dawkins doesn't.  Gould didn't.  Sagan didn't.  Right.


Really?  What makes you think that Pasteur, Newton, and Mendel discounted scientific observations that were not the result of laboratory observations?  Newton used experiments where he could to validate his theories, but he also relied on verifiable observations of nature.  Similarly, evolutionists have proposed experiments to validate natural selection, but they also rely on information from natural observation as well.  Your use of experimentalism requires that you treat natural observation as somehow less important to science than lab experiments.  That's absurd, since many scientific theories do not lend themselves easily to controlled lab experiments--e.g. theories of astronomy and geology.

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"Science attempts to understand observations about nature, and not all scientific theories are equally amenable to laboratory experiments."

Well, that is certainly true, isn't it?  lol  That's pretty much the point.  Do you deny that there is not an epistemological difference between something that is directly observed as opposed to something that is inferred, instead?  The inference may be reasonabe:  assume it is for the purposes of this question.  Is it really your position that the two are of the same epistemological value?


That depends on what you instantiate for "something".  Scientific observations are those that are dependable or repeatable.  Nowadays, scientists also model or simulate theoretical properties in computers in order to generate predictions that can be confirmed through observation.  Newton and his contemporaries pioneered the methodology by the use of mathematical models.  Today, we use computers to prove theories that were beyond proof before the computer era.

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"Calling yourself an "experimentalist" strikes me as a bit strange, because you have never really conducted scientific experiments yourself, have you?"

I'm not really sure what you mean by this.  Haven't we all conducted SOME scientific experiments, even if they were only in high school physics class?  I know I did.  I presume instead you mean that I haven't conducted the empirical (I'd rather not use the word 'science' because that is question-smuggling) experiments for a great many things considered to be reliable facts of nature.  Obviously I haven't.  But neither have you...


Actually, I have both conducted my own experiments and participated teams that were conducting experiments.  For example, I once participated with a neurologist and another linguist in an experiment to determine which muscles were being enervated during the production of nasal vowels.  There was a rigorous methodology that had to be followed.  (Although I was the grad student at the time, I convinced the lead professor to have the wires injected in to his own soft palate.  He was British, so he was a sucker for doing painful experiments on himself.  :-))  It's true that you should have been exposed to some scientific methodology in high school, but it still seems strange to use that as a basis for calling yourself an "experimentalist".  As I said before, I think that you are just staking out an artificial epistemological position that you think will help you dismiss the scientific underpinnings of evolution theory.  It may work for you and other folks looking to dismiss evolution, but I expect you to make little headway in convincing others.

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Similarly, scientists today don't get a pass, either.  If I cannot re-create their experiments, what am I to do?  I am not powerless.  Do they have an agenda?  Do they have a bias?  Do they have philosophical pre-suppositions?  How much of their experimental conclusions interacted with this philosophical material?  Did they take steps to winnow out such things?  It is helpful if other scientists corroborate the experiment- but if they share the same dispositions I may have reason to remain skeptical.


It is just a little bit hokey to dismiss a scientific consensus on allegations of bias.  Science is based on a wide range of published data, including both natural and laboratory observations.  There are always scientists willing to pursue observations that disconfirm theory, because that is a wonderful way to get publications.  If the observations can be made to conform to theory, then that's a winner.  If they can be shown not to conform, then that's also a winner.  Indeed, science is all about testing doubts.  Religion is all about suppressing doubts.

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The primary assumption sitting underneath science today- especially present in evolutionary science- is that the data absolutely must be interpreted in a naturalistic framework.  It does not surprise me, therefore, when scientists are able to interpret their data in a naturalistic framework!  But what if the whole question was whether or not this assumption is really reasonable and rational?  You cannot prove it is reasonable and rational while simultaneously assuming it.


I thought you said that you weren't interested in changing the definition of science.  Scientific empiricism is all about physical observation.  You want to go beyond that.  Nobody's stopping you.  Let your speculations take you where they will.  Just don't blame scientists if they refuse to get dragged off their feet by your hot air balloon.  ;-)

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The theory of evolution forbids itself from considering non-agency interpretations of the data.  To the extent that scientists think they are doing a great job of continuing to interpret the data in light of that preclusion, I commend them.  Human imagination knows no limits.  Is it 'scientific'?  I hardly care.  Is it true?  THAT I care about.  And I don't happen to give much weight to claims that rule out certain interpretations out of hand, regardless of whether or not some think that is essential to their methodology.


Science does not "forbid itself from considering non-agency interpretations of data".  It forbids itself from considering explanations that are unconfirmable.  If you "agency interpretation" can't be confirmed by observation, then science cannot endorse it.  Sorry, but there are plenty of scientists who manage to separate science from religion on that basis.  You seem unable or unwilling to do that.  Hence, you campaign vigorously to have religious opinions addressed in science classes.

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"I believe that we've both established that evolutionary theory has been used to explain the origin of the Golgi complex, and the web sites you found seem to support that claim."

lol, the 3 web sites?  On the one hand, no, I do not agree that the GA has been explained by the TOE.  Clearly scientists think that it can be.  But there is a chasm between 'can be' and 'is.'


I think that scientists would be happy to substitute "can be" with "is".  There is nothing about the Golgi complex that suggests a non-evolutionary origin, is there?  Are we talking "Intelligent Design" here?  Are you picking this one out from the ID literature?  (You claimed not to read the "creationist literature", but you clearly do not consider ID a creationist movement.)

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"Maybe you can help the process by explaining what you are hoping to show by this line of argument."

Quite simply:  Genetics forms the basis for understanding biology, not evolution.

Genetics is all about experimentation, baby.


What if one were to maintain that "Evolution forms the basis of understanding genetics"?  Since "forms the basis of" is a transitive predicate, we have a logical proof that "Evolution forms the basis of biology", and your "not evolution" tag can only be justified if you can refute the claim that genetics is based on evolution theory.  Biologists seem to think that it is.  See, for example, the web page Evolutionary Genetics.

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Not only that, but I can go about my life.. if I were a doctor, a biochemist, a pharmacist, whatever... completely competent on the understanding based on the actual observations without even a glance at any alleged 'explanations.'


Not true.  You would not get a higher degree without demonstrating competence in basic biology.  Once you have your license to practice applied science, you might not need to consult theoretical models, but you may need the background knowledge at times in order to understand the medical literature and participate in professional discussions with colleagues.

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That is why I mentioned the people that I did.  Apparently quite a few actual biologists find it unhelpful, too.  Did you fail to note my reference to the biochemist who worked at a major drug company?  Evolutionary theory was completely irrelevant.


My father, mother, and brother were pharmaceutical chemists who worked for drug companies.  My sister is a tenured professor of clinical chemistry.  I have never heard such a claim from them.  They have never expressed any doubts about evolution theory, but I'm sure you consider yourself better informed.  I'm not sure that they have needed to appeal directly to evolution theory in any of their professional work, but that would hardly surprise me.

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"It all depends on what you think needs explaining."

Bingo.  But experimentally speaking, not everything can be explained.  That doesn't mean you get to make up explanations based on your presuppositions.  If the experimental data is limited- that's life.  Deal with it.


I've got no problem with that, but you evidently do.  If scientists rely on non-experimental observations to confirm theory, that too is life.  Deal with it.  :-)

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I was speaking of the category of 'evolution' that the ecologists I've read will cite.  Microevolution may be the mechanism that ya'll think justify macroevolution, but it nonetheless remains that you can dismiss macroevolutionary 'explanations' altogether and still function just fine.


Again, that depends on what you need to explain.  There are many people in the world who do not need knowledge of biology in their daily lives.  That is irrelevant to the claim that biologists need evolution to explain their science.
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« Reply #45 on: June 14, 2006, 03:18:58 PM »

Quote from: Broken
Quote from: sntjohnny
"Heh. William Purves book is an intro-level biology text written for High School students."

So sorry, Broken.

UCLA uses it:
http://www.lscore.ucla.edu/ls1.html

Its used at Reed College:
http://academic.reed.edu/biology/courses/BIO263/

Here it is at a British college:
http://lib5.leeds.ac.uk/rlists/biology/blgy1211.htm

And here it is at flippin A God Almighty Yale:
CLICK HERE

That's the google cache.  It seems they have restructured their site.  I couldn't find a link for course home pages to see if they still use the book or not.  That link is for summer of 2005.  at YALE.  Sometimes its embarrasing to see how far people will go to try to marginalize others.


From the Amazon review of Purves's book:

"His clear explanation of the concepts with bright, colorful pictures have helped my students to understand biological concepts for the AP Bio exam as well as preparing them for college."

Whether used as a high school or freshman college text, we are still talking very intro-level biology. Molecular Biology majors will typically take many additional courses in molecular biology, eukaryote and prokaryote cell biology, biochemistry, molecular genetics, immunology, and virology. And that is just at the undergraduate level.

So, to claim that the lack of detail on transposable elements (TEs) in a basic book like Purves somehow makes the subject of TEs unimportant is just silly.

TEs are highly interwoven into our genomes and, in fact, represent over 40% of our total DNA. These parasites are rapid mutators, integrate themselves into the genes of all plants and animals, and are a major evolutionary force.

Viral and plasmid TEs are also responsible for transmitting genetic material between unrelated species. In the book by Fred Bushman I mentioned earlier, Lateral DNA Transfer, (Amazon LINK), his lead-off example is rather astonishing (from a reviewer):

One example of lateral DNA transfer concerns marine bacteriophages in the oceans. Each milliliter contains on the order of ten million viruses, most of these being bacteriophages, which infect bateria. When these phages grow, some of them pick up the genes of the host cell and transfer them via infection to a new cell. The transferred sequence then can become stable, and from experiments this happens one out of 100,000,000 times. Due to the vast size of the oceans, this translates into 2 million billion lateral DNA transfers per second!

Rather thought provoking, to think of the ocean as a gigantic genetic super-computer. Makes you wonder what genetic program is running out there, doesn't it?
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You do not need either evolution or creationism to understand these things.  Let's look at this paragraph in more detail:

"Does the mitochondria example ring a bell? The fact that the mitochondria in our cells reproduce like bacteria, have bacterial genomes, bacterial ribosomes, and have gene sequences closely related to certain invasive bacteria which they physically resemble is difficult to explain except by evolution. You certainly have never provided a Creationist explanation."

You don't need an 'explanation' to understand what is being observed.  In your paragraph you resorted completely to genetics.   We have different notions at work here.  You think you've done something impressive if you've 'explained how.'  That's why you think I need to offer a 'creationist explanation.'  This is far from the point.  The only reason anything needs to be explained in the first place is because the genetics are known in the first place.  You don't need to have a theory on 'how' the mitochondria got here in order to understand the genetics of how it is.


Sorry, but if your theory cannot account for known facts, it is not a valid theory of science. At least give it a shot.

Here, I'll help you: maybe the "Creator" just got tired of building life from scratch. So He scooped up some rickettsia bacteria, tinkered a little bit, stuffed them into our cells, and presto-chango, instant mitochondria! OK, not very plausible compared to the evolutionary explanation, but at least I tried.
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Certainly, except for 'mitonchondrial eve' type theories which seek to expand on this alleged 'how,' I doubt you could provide me any meaningful examples why thinking of the mitochondria in evolutionary terms, rather than genetic terms, is the key to understanding the mitochondria.

Don't confuse "mitochondrial Eve" genetic tracing with the symbiogenesis of mitochondria. Entirely different subjects.

Don't confuse yourself by thinking evolution and genetics are somehow separate subjects. They are joined at the hip, especially at the molecular level. You can't understand genomes without evolution and you can't understand evolution without understanding genome dynamics.

You ask why thinking of mitochondria in evolutionary terms is useful. Simple. The closest relative to mitochondria are rickettsia bacteria, a gram-negative obligate parasite which lives inside eukaryotic cells (just like mitochondria do). The main difference is that the mitochondria's genome has atrophied down to just those genes the host eukaryote cell can't provide. So, if you want to understand why mitochondria are structured the way they are, study rickettsia. Pretty useful, no?

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"Or how about the broken vitamin C gene in apes and humans? The exact same gene broken in exactly the same way in exactly the same spot. How do you explain it except by common ancestors?"

Genetics.  Without genetics, you wouldn't even know that anything was the 'same.'   Don't you see where the problem is in your whole approach?  

"Also in ape and human genomes, virus genomes inserted in exactly the same spots in our DNA. Also, the amalyse gene with a retrotransposon inserted in the very same spot in the genomes of all old world monkeys, including us. How do you explain these phenomena except by common ancestry?"

Man, that's an awful lot of genetics in there.  Why should it need an 'explanation' ?   You can know all the things you said above without having any need to invoke an explanation.  They are simply brute facts that you can observe.  You gain nothing by drawing an inference about the source or origin that cannot be gained by simply sticking to straight genetics.


Lame. The conclusion of molecular genetics is that the only plausible explanation to the "matching mutations" puzzle is that humans and apes had common ancestors. Here's why:

From the genetic analysis, humans and apes have many of the same mutations. Some are negative in effect, such as the identical vitamin C gene mutation. Some are positive, as with the TE inserted into the amalyse gene. However, the probability of human and ape genomes having multiple mutations of exactly matching types, in exactly the same genetic locations is about the same as you winning the lotto three times in a row. In other words, zip.

So how did these identical mutations come about? The only answer compatible with molecular genetics is that apes and humans share a common ancestor who already had these mutations in their genomes. If you can find a molecular geneticist who disagrees, let me know.

So, your feeble dodge aside, the actual genetics answer to the "matching mutations" puzzle is common ancestry. I am still waiting for your Creationist answer. By the way, here is a Creationist making an honest  attempt to answer the very same question: LINK. Perhaps he can help you.

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"I look forward to your usual dodging, followed by your usual mental deletion or denial of all information contradicting your view of reality."

There is no dodging.  My argument is plain:  you cannot understand biology without genetics.  You can understand it without evolution.  Evolutionary theory moved to accept Mendel.  Mendel did not move to accept evolutionary theory.

Simply waving the word "genetics" around is not an answer to the "matching mutations" puzzle. It is just another dodge. The Creationist I linked to above made SOME attempt to provide a creationist answer.

By the way, genetics science has moved light years beyond Mendel, even light years beyond Watson & Crick. Evolution is essential to molecular genetics. Genetic recombination is a reality, whether by hybridization, transposable elements, or lateral DNA transfer. Genes are built from these evolutionary mechanisms. This is directly observable, in the laboratory.
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I am now on my second reading of this college text book.  It begins with genetics and doesn't stop with genetics until about page 425.  It would seem as though genetics is an important part of biology.  :)  Finally, after 400 pages of discussion about genetics, it finally gets to evolution.  The really funny thing is that in this book allegedly on biology, the arguments it draws on for that part are based on geology, not biology.  Too funny.   Then, beginning on page 450 (The Mechanisms of Evolution) it is back to genetics until page 500.


It is good that you are educating yourself. I am sorry your text has so little on evolution. Instead of re-reading Purves, try Campbell and Reese, which is the dominant first text for biology majors, with a heavy emphasis on evolution. Then move on to Bruce Alberts, "Molecular Biology of the Cell".

Also, Frederic Bushman's "Lateral DNA Transfer" is very readable even without a strong molecular bio background. If you really want to take on the evidence for evolution, read this book.

Besides, it covers some real thought-provoking subjects: how bacteria acquire resistance to antibiotics, how genetically modified crops can pass their new genes to other plants, how viruses can hop from birds to humans, and a lot of other relevant stuff
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