Monday, December 27, 2010

Re: Genetics Book

Re: Genetics Book Hey Brandon,

Sorry I came across in such a negative manner—I certainly didn’t intend to.  I was in a hurry when I wrote my last email, so perhaps that’s why the tone was a little off.
 
I’m thinking that reading this genetics book will help us find some common ground,  at least as far as terminology, which should be very helpful.  

Though I don’t always appear enthusiastic, I do always enjoy learning. :)   And I do want to make sure that what I’m learning is true.

In particular, you claim that there is no such thing as a neutral or nearly neutral mutation. Well, the chapter on gene mutations shows exactly the mechanism by which a mutation can occur with absolutely no effect on the phenotype of the organism.
Of course a mutation can appear to have no effect on the phenotype of the organism.  Mutations can affect body processes which aren’t outwardly apparent.  If the mutation concerns something that will only be activated under certain conditions, that mutation may just sit there with no apparent effects on phenotype—until those certain conditions occur.  Remember, genotype and phenotype aren’t the same.  Another thing, organisms have built in corrective mechanisms which are able to ‘fix’ many mutations before they have a chance to cause harm.   Both the books I sent you—Signature in the Cell and Genetic Entropy—address this issue of neutral or near neutral mutations. (The second is a little more direct, while the first one talks more about ‘junk’ DNA, which is supposed to be a conglomeration of mutations which have collected over time.)  I’m looking forward to seeing how they compare with the book you recommended.  Our discussion will go much better if you study the books I sent you while I study the one you recommended to me.

Since I'm on a roll, there's something that's been bugging me for a while. It's your argument that runs along the lines of "if everyone jumped off a bridge, would you?" I point out that the overwhelming majority of scientists across the globe point agree that evolution is correct, and you say "well, they could all be wrong." Of course you could be right, and all those scientists could have been wrong for 150 years, but would you at least admit that a vast scientific consensus on a hotly debated topic probably means something? To say that  a scientific consensus doesn't convey any information at all in nonsensical. 
I’ll concede that if most scientists agree on something, it is more likely to be correct.  HOWEVER, the fact that most scientists agree on something has nothing to do with whether or not that idea is correct, and scientific consensus is not a proof.  I can think of lots of ideas about which earlier scientific consensus was later proven to be wrong—the usefulness of the appendix and thymus, the need to wash hands and instruments between patients, the usefulness of leeches/bleeding to treat various illnesses, the perceived  causes and best treatments for various illnesses, and so on.  Today, some people claim that there is a scientific consensus, even when there isn’t one.  For example, there is no real consensus about ‘global warming’ (there may be more of a consensus that it isn’t happening than that it is).  And there are probably more scientists with a creationist perspective than you might expect.  It’s just that you might  not hear about them because they don’t follow the scientific PC thinking.  And another thing—if the majority of educational institutions are teaching evolution only, they are naturally going to produce people who think from an evolutionary perspective.  Some will be brave enough to think outside the box, but most will just absorb and reflect back what they have been taught.  And if they want to become research scientists, they know that they’ll be more likely to get funding if they couch their research in the framework of Darwinian evolution.

But! the statement "a theory is true implies most scientists agree it is true" is hopefully, for the most part, almost always true.
I think what you’re saying here is, “If a theory is true, then most scientists will agree that it is true.”  Is that correct?  If so, I would have to disagree.  For example, there was a time when most scientists agreed that the appendix was a useless appendage—those scientists believed something to be true which was, in fact, false.  In this case, the consensus opinion was in error.  The theory that the appendix is useful was true, but most scientists disagreed with that theory and chose to stick with the consensus theory.  Somewhere along the line, some scientists began to question the consensus opinion, did further research, and discovered the usefulness of the appendix.  Your statement would be in error every time a consensus idea was shown to be wrong.  

Yes, you believe that evolution is wrong, but stop acting surprised when you see scientists using evolution!
I’m never surprised when I see scientists explaining things from an evolutionary perspective—after all, that’s the way most of them have been taught.  What I take issue with is the idea that one must interpret everything from an evolutionary perspective in order to do good science.   Belief in Darwinian evolution isn’t necessary in order to do empirical science.  One doesn’t need to know exactly how we got here in order to study how things currently function in the present.  Creationists and Darwinian evolutionists use forensic science, which is a whole nother ball game.  I also take issue with educational institutions and scientists treating the theory of Darwinian evolution as if it were a fact which must never be questioned and need never be explained—it seems to me that such an attitude would tend to discourage critical thinking.

I like long emails. :o)  The more you write, the better idea I have of how you’re thinking.  It also makes me feel more connected.  Wish you didn’t have a cold and were closer to family—I like being around family for Christmas.  It actually snowed here on Christmas day—five inches—not much compared to Boston, but more than we’ve had since moving here over a decade ago.  I read online that this is the first time Georgia and S. Carolina have had snow on Christmas since the 1880’s.

Take care,

Susan

Re: Fossil Finger DNA Points to New Type of Human | Wired Science | Wired.com

Re: Fossil Finger DNA Points to New Type of Human | Wired Science | Wired.com Hey Brandon,

It’s disconcerting that the article ( http://m.wired.com/wiredscience/2010/12/denisovans/ ) opens up talking about a finger bone, but displays a photo of a tooth.  

> However, kinetic calculations predict that
> small fragments of DNA (100–500 bp) will survive for no
> more than 10 kyr in temperate regions and for a maximum
> of 100 kyr at colder latitudes owing to hydrolytic damage
> (Poinar et al. 1996; Smith et al. 2001). Even under ideal
> conditions, amplifiable DNA is not thought to survive for
> longer than 1 Myr.
> http://rspb.royalsocietypublishing.org/content/272/1558/3.full.pdf+html?sid=1c
> ad9280-7246-49eb-b212-6f6358028c5e
This article discusses the viability of DNA over long periods of time.  It finds that DNA in dead organisms degenerates over time, so that what appears to be indicating DNA of a different species may in fact simply be the product of postmortem degeneration.  It’s also interesting to see that identifiable fragments of DNA would not be expected to survive over 10,000 years in a temperate region (where this part of Siberia is located).  These findings fit much better with the biblical creation scenario than with the 40,000 years mentioned in the wired.com article.   

Much of the rest of the article is conjecture based on interpreting evidence from an evolutionary perspective.  I wonder how these scientists are defining ‘species’, since they acknowledge that these early humans probably interbred with other human populations.  It would make more sense to describe these people as a different strain or variety, like the Australian aborigines or Eskimos—assuming that the DNA differences found aren’t simply the result of postmortem degeneration over time.

Susan

Sunday, December 26, 2010

Re: Genetics Book

Hey Susan,

I.

In your email you said: "If your book assumes Darwinian evolution does not need to be explained or proven, it may not be that useful to your argument.  We'll see.... :o)"

I just wanted to point out that I don't want us to read this book expecting that the book will sway us one way or the other. I expect only that we will learn the language necessary to discuss mutations intelligently. That is what I said I wanted to do the first time I brought up us reading a textbook on genetics, and I have not branched away from that goal.

Of course, I expect that a better understanding of genetics will only serve to strengthen my arguments and be a detriment to yours, but that's only because I think I'm right and you're wrong:)

II.

Also, I'm a little bummed that you're not reciprocating (or acknowledging;) my excitement over the chance to learn awesome stuff at the forefront of science! I nearly waxed poetic about it, and all I got from you was a ho-hum response. Very disappointing. I thought you were all about learning (more) about genetics with me? I mean, come on, the most advanced genetic argument we've brought to bear so far has been a fuzzy anecdote about Mendell's peas! This is gunna be an exciting new chapter in our evolution debate. Let's get pumped!

III.

As I've said before, I don't think there is any one test that will prove that evolution is true. It is a major scientific theory (like germ theory or the theory of gravity) that can only be shown to be correct with many small tests that confirm expectations. You have proposed that some (or all) of those tests are incorrect. You have also proposed that some of the basic assumptions of evolutionary biologists are incorrect. And hence we debate. I think that knowing more about genetics will help us to resolve some of these conflicts.

In particular, you claim that there is no such thing as a neutral or nearly neutral mutation. Well, the chapter on gene mutations shows exactly the mechanism by which a mutation can occur with absolutely no effect on the phenotype of the organism. Also, this mutation is a very simple one for which there is no reason to believe it doesn't occur regularly. You can read the chapter for yourself to find the example, or if you'd like me to explain it, I'd be game. 

Now, once again, I'm not trying to prove all of evolution. I am focusing down on one very simple argument that you have: that neutral mutations do not occur. I feel that this argument is now defunct. Do you agree? 

Or maybe I misquoted you, and maybe your argument was more nuanced than that, but would you at least agree with the statement, "Neutral mutations do occur"? (I'm working really, really hard here to find some common ground between us, a place from which we can start moving forward.)

IV.

Since I'm on a roll, there's something that's been bugging me for a while. It's your argument that runs along the lines of "if everyone jumped off a bridge, would you?" I point out that the overwhelming majority of scientists across the globe point agree that evolution is correct, and you say "well, they could all be wrong." Of course you could be right, and all those scientists could have been wrong for 150 years, but would you at least admit that a vast scientific consensus on a hotly debated topic probably means something? To say that  a scientific consensus doesn't convey any information at all in nonsensical. 

It's just a nice logical construct. The statement "a theory is true if and only if most scientists agree it is true" is clearly false. But! the statement "a theory is true implies most scientists agree it is true" is hopefully, for the most part, almost always true. This is especially true of theories that much, much work has been put into (and less true about theories that relatively no work has been put into). To claim that it is false is to claim that the scientific method doesn't work. 

My only point here is that you might be right, and almost all of the scientists in the world could be wrong, and evolution could be a sham. But you'd have to agree (I hope) that this would indeed be a rare occurrence. Do you agree?

V.

Tangential to that last part is me about to go out on a limb. In response to your repeated comments that this or that author is working from the premise that evolution is true, I say, of course they are! Almost every single scientific work in the entire world involving biology uses evolution as a fundamental tool! This does not throw out the impartiality of the biologists any more than astronomers assuming the theory of gravity is true does theirs!

Yes, you believe that evolution is wrong, but stop acting surprised when you see scientists using evolution! Is that so much to ask?

VI.

Well, this was a really long email. I hope your holiday season is going well. Mine has been laid back what with a lingering cold and no family to run around with. I'm going to try to get back into the swing of studying tomorrow. Wish me luck!

Thanks,
Brandon

On Sun, Dec 26, 2010 at 8:39 AM, Susan wrote:

Hey Brandon,

I ordered the genetics book (but not the solutions manual) you suggested—will be interesting to compare what it says with the book I sent you (Signature in the Cell).  From what you've described, it sounds like your book is operating on the premise that Darwinian evolution is a fact which does not need to be explained or proven.  If so, it would seem to discourage critical thinking on the topic.  Hopefully, the book's approach to basic genetics will be more objective.  

Our primary discussion is on whether Darwinian evolution is the mechanism by which all life was formed and developed, from non-life to life to the huge variety of organisms present in today's world.  If your book assumes Darwinian evolution does not need to be explained or proven, it may not be that useful to your argument.  We'll see.... :o)

Hope you've had a wonderful Christmas weekend!

Susan

Saturday, December 25, 2010

Genetics Book

Hey Susan,

I finally got Jonathan to pull out his undergrad text on genetics for me (it was sitting on the bookshelf with GENETICS written down the spine...duh). It's pretty awesome. It's clearly written and has tons of diagrams and riveting examples. It's nice to read an undergradate text book after having slogged through so many graduate level math text books. It's just less dense and there's a focus on clarity that's refreshing.

Anyways, I hope you'll read along! The book is called Genetics: A Conceptual Approach (second edition) by Benjamin A. Pierce. The ISBN is 0-7167-8881-0 for text only and 0-7167-6836-4 for the text and solutions manual CD. Jon does have a solutions manual that comes with a CD, but I haven't looked at that yet. You might get that too if you're very interested. I looked on Bookfinder.com, and you can find the text book (used) for about $5 including shipping. Amazon seems to have about the same pricing. 

I've already read Chapter 9, which is about chromosome mutations. It was really interesting. Did you know wheat has 6 sets of chromosomes while we only have 2? Crazy. I'm now reading Chapter 17 on gene mutations.

The book has clarified a lot of the vague ideas about mutation that I had before. In particular, it's clarified for me the distinction between selective breeding for characteristics in order to accentuate recessive genes versus breeding to select for novel mutations that crop up. I think this distinction is very important for understanding natural selection and evolution. 

The book does have a couple chapters devoted to evolution, and I'm excited about reading those, too. I imagine it will cover the precise genetic mechanisms by which natural selection and evolution occur. I imagine those chapters will stick in your craw a little bit, as will all the sprinkled references to evolution in the rest of the book. I hope those things won't get in the way of you seeing this book for what it is: a text book explaining genetics (that is used at one of the best undergrad biology departments in the world). I think that with a better genetic vocabulary, you and I will be able to better debate the evolution issue. 

I'm also excited about reading chapter 2 which describes the form and function of chromosomes in detail. I also clearly don't know (or remember?) enough about the stages of meiosis and mitosis (prophase 1?? disadjunction??). So I look forward to reading about those. Also, the shapes of the chromosomes kind of intrigue me. I mean, what a funny shape for something that's basically a really long tape of 4 letters! Why does the DNA wrap itself up in this funny bar shape, and why do two bar shapes connect with each other at a "centromere" to make an X shape? And on another tack completely, if only one X chromosome is read in each of our cells (and the other X chromosome shuts itself down into a "bar body" in women), why does only having one X chromosome give men their distinctive features? There's so much to learn! Very exciting.

Later,
Brandon


Friday, December 24, 2010

Rapid evolutionary innovation during an Archaean genetic expansion : Nature : Nature Publishing Group

Um, this is a super complicated abstract, but Ben thought it was neat; so I'm passing it on. I think it's interesting that there's a way to look at modern genomes to get an idea of the genetic history of archaea. Well, after saying that out loud it seems obvious. I must be sleepy.

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09649.html

-b

Sent from my iPhone

Fossil Finger DNA Points to New Type of Human | Wired Science | Wired.com

This is a pretty interesting article about a distant relative:) Thanks Ben!

http://m.wired.com/wiredscience/2010/12/denisovans/

-Brandon

Sent from my iPhone

Friday, December 10, 2010

On studying the opposition

On studying the opposition Hey Brandon,

It would be good if you could get away from Dawkins as your primary defender of Darwinian evolution—there are just too many places where he presents a weak logic or ignores scientific observations/facts which do not align with his perspective.  It would also be good if you’d read books from the opposing view—read them in detail, not just skim over.  The book I just sent  (Signature in the Cell) would be very informative, and here are some other possibilities which address the relationship between science and Christianity:  

Stanley Jaki, The Origin of Science and the Science of Its Origin
Robert K. Merton, "Science in Seventeenth Century England," Osiris, 1938, pp. 360-632
Gary Parker, Creation: Facts of Life.  Author is a former evolutionist.

No need to reject them by saying such things as “they’re boring”, “the authors are biased”, or “the authors don’t know what they’re talking about”.  These sorts of rejections (which are logical fallacies) only tend to suggest that you either haven’t read the books, haven’t read them with the purpose of truly trying to understand them, or are depending on someone else’s opinion to guide your thinking rather than coming to your own conclusions.

I realize that you won’t have the time to read a lot of books.  However, it would be better to read one or two of these books thoroughly enough to make intelligent comments, than to brush over them simply because you don’t like their perspective.  And if you don’t study the opposition, how will you know that you have a rational argument for your own position?

Susan

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