Re: 2nd law again

From: Susan
Date: Mon, Jul 11, 2011 at 3:00 PM
Subject: Re: 2nd law again
To: Brandon 

It was a pdf file, which I attached to the email—guess that didn't work for the blog.  This should be the link:  A second look at the second law <http://www.math.utep.edu/Faculty/sewell/AML_3497.pdf> .  

Susan

2nd law again

Hey Brandon,

Attached is an article about the 2nd Law of Thermodynamics and evolutionary theory.  There’s also a back story to this—it was peer reviewed and accepted by a math journal, but the complaint of one blogger caused its acceptance to be rescinded.  The author complained and received an apology and compensation for legal expenses.

Susan

Re: Are Dog Breeds Actually Different Species?: Scientific American

Hey Brandon,

Have you ever been around when a batch of 17 year cicadas were hatching out?  It’s happening here, now, and they’re an extremely noisy bunch of insects—they’re fairly quiet early in the morning, then as the day warms up, they become more active, making a loud, undulating whine in the trees, sometimes seeming very close, sometimes further away, and often both near and far.  Sometimes, when I’m walking outside, their sound feels like a constant almost mind numbing roar; this has been going on for at least a week.  And while the cicadas are making their noise, the crickets chime in periodically, and of course, birds are singing everywhere—it’s a regular cacophony of sound.  Every so often the tree frogs add their voices, too.  (I wish I could identify more birds by their songs—I do much better by sight.)

So you claim that adaptation and change can happen "within a kind," but that one "kind" cannot change into another. The major problem with your argument is that you don't define "kind." 

Actually, I don’t think that’s a problem at all.  The classification of organisms is a bit arbitrary and subjective, and even Darwinian evolutionists can’t agree on how to classify some organisms, especially now that organisms can be studied to the level of DNA.  And evolutionary scientists also don’t all agree on the definition of “species”.  Somewhere I read that “species” was originally just another word (from Latin, I think) for “kind” and was simply a descriptive term, but the word eventually became an official scientific term related to taxonomy.  This is an area in which scientists still have much to learn, so neither creationists nor evolutionists can be totally adamant about which organism fits within which category, whether  the evolutionist’s “species” or the creationist’s “kind”.  In general, I’d probably say that if animals can reproduce with each other, they’re of the same kind—for example wolf and dog, or different breeds of dogs.  I don’t know about foxes and coyotes because I don’t know if they can interbreed with dogs. Cats and dogs definitely don’t interbreed, so are of different kinds.

The point we’re discussing, though, is whether one type (kind/species, whatever) can morph into another type, which then morphs into something else, starting from one-celled organisms and ending up with man.  Darwinian evolutionists assert that this can happen.  Biblical creationists assert that, while variation and adaptation within a kind occurs, one kind does not change to another kind—the canine ‘kind’ does not morph into the feline or bovine ‘kind’, nor does the ape ‘kind’ morph into the human ‘kind’.  Of all the studies I’ve seen presented by evolutionists, none have shown how one kind can develop from another.  Darwin’s finches always remained finches.  None of the thousands of generations of fruit flies that have been studied have yielded anything but fruit flies (many of which were grossly mutated, but they were still fruit flies).  Of the thousands of years of farm husbandry, farm animals have always produced after their kind—bovines produce bovines, swine produce swine, and so on.  In the studies of viruses and bacteria, the virus remained a virus, and the bacteria remained bacteria.

From a biblical creationist perspective, all the basic kinds of organisms appeared during the creation week at the beginning of time (Genesis 1).  Mankind was made last and separately from all the other creatures.  While there is no specific list of all the ‘kinds’ of organisms, it does say that each organism is to reproduce after its own kind:  “Let the earth bring forth grass, the herb that yields seed, and the fruit tree that yields fruit according to its kind...” (Genesis 1:11)  Likewise, the birds, sea creatures, and land animals were each created according to its kind.  Just as apples always produce apples (and not peaches or beans), bacteria, molds, mammals, and humans each reproduce according to its own kind.

As for dog coats, you give one explanation for where the three genes come from: that God put all three genes and their variants in wolves, and people selected for them. Another explanation is the evolutionary explanation: that wolves had a certain set of genes, and as they were being domesticated, some of the wolf offspring had mutations in those genes that gave them coats that humans found charming. Then humans selected for these. And each time a new, charming mutation occurred, humans selected for it.

You’re apparently assuming that wolves were the first of the canine ‘kind’--how do you know that?  Yes, I’m saying that the three basic genes were present from the beginning, and then variation resulted over time, whether due to human intervention or environmental conditions or other factors.  That article stated that most variation could be accounted for by the mixing and matching of these genes.  Mutation probably accounts for a small portion of the variation.  For example, I believe the Mexican Hairless breed is the result of a mutation, as is presence of skin folds in sharpeis.  Of course, in both breeds, negative traits go with the mutations—both breeds have ‘weak’ skin very prone to infections and allergies.  Even with these mutations, sharpeis and the Mexican Hairless are still dogs—mutation changed some traits, but did not change their basic canine genome, the genes that make them canine rather than feline or something else.

It is mutations of genes that give the variety we see!

On what do you base this statement?  Are you saying that these three genes for hair coats are all the result of mutations over time, and that there was a time, before the appearance of these genes, when all canines looked the same?  And if these three genes weren’t present in the earliest canines, what determined the appearance of their coats?  You’re making this statement as if it were a fact when, in truth, there is no way you can be sure of this.  It appears that you are observing something in the present (presence of three genes for canine hair coat) and then interpreting its meaning about the past (that those genes appeared through mutation over time) from an evolutionary perspective.  The study in the article used empirical science to learn about these genes; it determined how these genes function now, and while it determined that these genes account for most of the variation in canine hair coat, it says nothing about where those genes originally came from.   

Apparently you believe that all wolves and dogs are related. How bout foxes? Coyotes? Are all birds related? Are bats related to birds? How can you tell? What about all apes? Are the monkeys related to apes? How bout bushbabies? (cuz they're super cute) Are camels related to horses? How can you tell? How do you know cats are not related to dogs? You seem pretty confident.

What do you mean by “related”?  Most of these animals are classed as mammals because of morphological similarities.  And these mammals are classified into various sub-groups on the basis of morphology.  They are “related” in the sense that they have similar characteristics.  But similar morphology doesn’t mean these animals are “related” in the sense of having shared ancestors.  Bats are mammals that fly—they’re probably their own ‘kind’.  I would also say that camelids, equines, felines, and canines are each different ‘kinds’.  I imagine there are multiple ‘kinds’ of birds just as there are multiple ‘kinds’ of mammals.  You seem fairly confident that all organisms are related through heredity in some way—on what are you basing your confidence?  

I wish I could understand your integral that you wrote up.  It may be trivial, but I think it’s neat that you have the knowledge to be able to write it.

Glad to hear you’re trying to keep some balance in your life by setting boundaries on your work.  :o)

Congratulations to VJ!  Didn’t know the major he chose existed—will he use it in his current job?

Susan

Re: Are Dog Breeds Actually Different Species?: Scientific American

Hey Brandon,

Thought I’d send a few thoughts about that article, on the off chance that you might actually welcome a little conversation... :)

Creationists argue that speciation has never been seen.

The taxonomy of organisms is somewhat subjective.  Scientists don’t always agree on how organisms ought to be classified.  What does he mean by saying creationists argue that speciation has never been seen?  Creationists have no problem with variation within a kind, such as all the different sorts of canines.  It appears that the author wants to use the word speciation (in regard to the wide variety of dog breeds) in a way that misleads people into thinking that creationists do not believe that variation and adaptation occur.  

For that matter, how does the author define ‘evolution’?  If he’s merely defining it as ‘genetic change’, as the genetics book you recommended to me does, that definition is so broad that it would cover almost anything, including such things as variations in eye color, hair coat, or beak size.  Again, creationists are fine with the idea of adaptation and variation within a kind.  What they have a problem with is the idea that one kind can morph into another over time— say from canine to feline or from amoeba to man.  

Take the many variations of hair texture, length, and color found in canines.  Scientists have found that they all come from variants of three genes.

Just by mixing and matching... these three different genes, we could account for most of the variation that we see in coats in domestic dogs http://news.bbc.co.uk/2/hi/science/nature/8224519.stm

In other words, the many variations were developed by mixing and matching genetic material that was already present in the dog genome—no new material evolved.  

Sometimes it would be nice to talk about something else.  I like the debate, but when that’s all we talk about it makes things feel too one-dimensional—there’s more to us than just this.

Susan



On 5/3/11 12:39 PM, "Brandon Meredith" <mathcadd@gmail.com> wrote:

> http://www.scientificamerican.com/article.cfm?id=an-immodest-proposal
>
>
> Sent from my iPhone

Genetics book

Hey Brandon,

Okay, I’ve gotten the genetics textbook and have started reading it.  You’re correct in saying the book won’t help much in our discussion on creation/evolution other than giving us a foundation for discussing genetics.  

I was hoping the book would say something about d- and l-isomers, but I  don’t think it does—at least I haven’t found it yet.  It then occurred to me that I might be more likely to find this in an organic or biochemistry textbook.  Since I still have some of my old textbooks, I looked in them and found it quite easily.  

The book’s definition of evolution:  “genetic change among members of a population.”  p.663  According to this definition, any change would be considered evolution.  This definition conflates adaptation (variation within a kind, which I have no problem with) and macroevolution (change from one kind to another, such as monkey to man, or even prokaryotes to eukaryotes).  The textbook appears to do an excellent job of explaining adaptation within a framework of genetics.  On the other hand, it seems to be a bit lacking in explaining the ‘monkey to man’ type of evolution within the framework of genetics. Of course, the study of macroevolution primarily involves forensic science, while this textbook focuses on genetics from an empirical perspective.

An excerpt from chapter 17, on mutations:  “Mutation is a fact of life.  Our DNA is continually assaulted by spontaneously arising and environmentally induced mutations.  The fact that most are detrimental is evidenced by the number of mechanisms that cells possess to reduce the generation of errors in DNA and to repair those that do arise.” (p.500)
So living organisms possess multiple mechanisms to correct mutations.  Yet the build up of mutations is supposed to be a driving force in Darwinian evolution.  I’ve not yet discovered from the book how the forward movement of Darwinian evolution is supposed to have overcome the resistance to change evidenced by the corrective mechanisms.

My results (Table 4) confirm several generally accepted facts about human spontaneous mutation: 1) well over 90% of all mutations are single nucleotide substitutions [Giannelli et al., 1999; Nachman and Crowell, 2000], 2) CpG context increases substitution rate by ~1 order of magnitude [Sommer, 1995; Nachman and Crowell, 2000], and 3) deletions are ~3 times more common than insertions [Gu and Li, 1995] so that mutation shrinks human genome by ~1 nucleotide per generation [Petrov, 2001]. [italics are mine] ...
The results reported here imply, in agreement with previous estimates [Vogel and Rathenberg, 1975; Kondrashov, 1988], that the total number of new mutations per diploid human genome per generation is ~100 (1.8 x 10tothe -8 x 2 x 3.2 x 10 to the 9=115). [couldn’t figure out how to make it write the correct symbols]

Kondrashov, A. S. 2003. Direct estimate of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation. 21 (1): 12-27.

What I find interesting in the above study is the statement that mutations shrink human genome over  time.  This flies in the face of the Darwinian idea that mutations increase genetic information and complexity.  If Darwinian evolution actually occurred, it would have had to overcome the loss of genetic information caused by mutations. [This study also seems to disagree with the genetics textbook in saying that most mutations are substitutions, while the  genetics book states that insertions and deletions are more frequent (p.477).  Since most of the references for chapter 17 are older than this article, this article is probably based on newer information than what was available for the book.]

In chapter 19, on genomics:  “The reduced DNA content, fewer functional genes, and the large number of pseudogenes suggest that, evolutionarily, the genome of M. Leprae has undergone massive decay through time, losing DNA and acquiring mutations that have inactivated many of its genes...  Regardless of the mechanism for gene inactivation and loss, this genomic decay helps explain some of the bacterium’s unique properties.  Genes for many metabolic enzymes and structural proteins have been lost, which may explain why the bacteria cannot be cultured on synthetic media containing traditional carbon sources; it may also account for the bacterium’s slow growth.” (p. 553)
Here, we’re talking about the degeneration over time of the genome of the leprosy bacterium.  I would call this genetic entropy.  The book says that this particular genome has deteriorated over time.  This poses a number of questions:  How did this bacteria evolve forward from non life or a simpler organism to become the leprosy bacterium?  What made this forward movement (from less complex to more complex) stop and begin to move backward (degenerate)?  If this genome has degenerated over time, why wouldn’t we expect any other genome to degenerate over time?  The Kondrashov study certainly indicates that the human genome has been degenerating (which agrees with the book on genetic entropy).  What scientists routinely observe is degeneration over time.  Where is the observation of the monkey to man sort of Darwinian evolution?

This is enough to begin with.  Since you’ve had more time to read the book than I have, perhaps you’ve already found answers to some of my questions.  And I’m sure you have questions of your own.  I’m looking forward to hearing what you have to say. :o)  

On a lighter note, snow is coming our way again—we’ve had quite a bit of cold and windy weather this winter.  Of course, I don’t mind as long as I’m inside with a cheery fire in the fireplace.  We’ve been keeping the bird feeders full, and it has been fun seeing all the different kinds of birds that show up.

Susan

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

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

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

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

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

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

Re: Media manipulation

I take it back! Its not a great article! It starts off great, but then looses cohesion pretty quickly. Still...watch those straw man arguments!

-b

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Media manipulation

Omg, I love Wikipedia. I think this is a great article. It reminds me of the dirty intellectual tricks that politicians pull while maintaining a straight face. You've brought up logical fallacies before. I was never explicitly taught them (besides circular reasoning). Anyways, I'm totally gunna call you on any of these logical fallacies if they crop up, so watch out!

Best,
Brandon

http://en.m.wikipedia.org/wiki/Media_manipulation

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Re: Fishy Teeth

Hey Brandon,

It appears that I’m not getting my ideas across very well.  I was trying to point out that evolutionary theory is irrelevant to making new discoveries, by italicizing words that showed evolutionary biologists were merely hypothesizing about something that supposedly happened in the past.   The questions about future research and applications could have been asked w/o these hypotheses.  I see nothing particularly predictive about  the work of the evolutionary biologists.  (Evolutionary biologists could easily pose whatever hypotheses they want in a way that would ‘predict’ present observations. That doesn’t make those hypotheses true, however.)  Any biologist can observe a network of dental genes in cichlids, and can observe the many variations in number and location of teeth in different types of animals in the present; and the questions asked in this paper, such as “Is tooth number regulated similarly across the pharyngeal and oral jaws?”  and “What are the relationships between genotypes and phenotypes?” could be asked by any scientist because they are based on observations in the present.  A scientist working from a creationist perspective would observe all these things and would still ask the  questions asked in this paper.  He would be prompted to ask them because he knows that God is intelligent, logical, and creative, and might be expected to use similar patterns for similar items (teeth in this case) in a variety of different kinds of animals. This is the same type of question the Christian chemist asked when he noticed that pattern of known elements and hypothesized the existence of not-yet-discovered elements, and then went on to search for, find, and identify some of those elements.  

What good was the evolutionary perspective when scientists, using evolutionary thinking, deduced that the appendix, thymus, and tonsils were useless evolutionary remnants?  How did that lead to scientific breakthroughs?

If the evolutionary biologist didn't actually help the geneticist in any useful way, do you think he would let them put their name on his paper? But he did.

This brings me to one of my pet peeves.  In general, there doesn’t appear to be much true openness to differing ideas in academia.  In the field of biological sciences, Darwinian evolution is the prevailing PC way of thinking, and scientists tend to couch everything in terms of it.  Students (at least for the last 40-50 years) are taught throughout school that Darwinian evolution is the only acceptable way of thinking about origins and science in general—most have little exposure to intelligent design or young earth creationism.  Evolutionary scientists would naturally tend to reinforce each other in maintaining that PC worldview.  (After all, they’re much more likely to get funding if they toe the so-called ‘party line’.)  Those who think differently—such as those who believe in intelligent design or young earth creationism—are denounced as not being good scientists, simply because they don’t hold to the prevailing PC worldview.  On top of that, evolutionists often criticize creation scientists for not having published many works, yet it is difficult for creation scientists to get their research published because it varies from the prevailing evolutionary thinking.  To me, that sort of narrow-mindedness will slow scientific advances, as it tends to keep people from thinking outside the PC box.  A scientist working from a creationist perspective might very well be totally ignored if he posed the same exact questions as were in the article, simply because the basis of his questions didn’t align with the prevailing evolutionary perspective.
 

As for specified complexity, surely it exists. But it is not part of the theory of evolution. And it is unnecessary when explaining biological form and function

Are you saying the specified complexity only exists in non-biological spheres, such as the designing and building of machinery, factories, and various kinds of modern transportation, where intelligent beings—humans—design the parts and specify how they are to be put together?   How about the specified complexity of language?  People are able to communicate because they can put letters (26 in our alphabet) into words, words into sentences, and sentences into books, creating works with very specific and precise meanings.  Letters never arrange themselves into anything meaningful.  Specified complexity isn’t part of the Darwinian theory of evolution because the proponents of the theory don’t want it there—after all, as you said, you’d have to believe in intelligent design in order to believe in specified complexity.  So, its absence in the theory doesn’t necessarily mean it doesn’t exist in the biological world—it just means that proponents of Darwinian evolution don’t want it to exist.

Dawkins’ explanations for why specified complexity doesn’t exist in nature are illogical and ignore what is already known in the fields of genetics and chemistry.  He ignores the problem of handedness—no mention of it in the chapter named Canterbury in The Ancestor’s Tale; he talks about Haldane’s “soup” of amino acids, yet never acknowledges that these weren’t truly living organic amino acids, but simply a mixture of artificially created amino acids of mixed isomers which could not possibly form into living RNA or DNA.  He asserted that a scientist’s experiment (Spiegelman’s test-tube world) demonstrates that things can artificially order themselves and replicate—yet this experiment was designed by an intelligent being, the scientist had to seed his test-tube world with pre-existing RNA  from another source (the RNA didn’t create itself in the test-tube), and the resulting strand of RNA kept getting shorter with each generation (a  good example of entropy or loss of information—quite the opposite of Dawkins’ idea of evolution).  Dawkins asserts that the appearance of design does not mean that there is a designer, even though in every other circumstance, any intelligent person would logically conclude that the presence of design does indicate there was an intelligent designer—especially since such a person would have observed things being created and have created things himself.  Dawkins acknowledges that DNA contains information (specific instructions for cellular function) in a language built from a 4-letter alphabet (p.20-21, Ancestor’s Tale), but never explains how language came to exist in the first place.  In the field of genetics, it’s known that DNA is self-correcting—there are mechanisms present which can repair much of the damage done by negative mutations,and Dawkins discusses it in the Ancestor’s Tale (p. 575)—yet Dawkins still asserts that cumulative mutations, supposedly present in ‘junk’ DNA, are a major factor in the evolutionary process.   Considering the many layers of complexity within even the smallest amoeba, the many parts that must coordinate perfectly with each other in order for the amoeba to live, what would be the mathematical probability that such a huge number of parts and functions would randomly develop themselves and combine into a living organism without any outside input?  I doubt that even billions of years would be sufficient.

It doesn’t help any that he makes such statements as “Evolution is now universally accepted as a fact by thinking people.” (p.308, Ancestor’s Tale)  And, “The first replicator worked de novo, ab initio, without precedent, and without help other than from the ordinary laws of chemistry.” (p.563, Tale)  The first statement assumes that only unthinking people accept creationism and that he knows what all people are thinking.  The second statement requires a great deal of faith (a religious concept), as neither Dawkins nor any other human was around when this first replicator supposedly appeared.  Dawkins simply created this idea in his mind, then believed it.  At least young earth creationists have the Bible, God’s message to mankind, on which to base their beliefs.

Enough for this letter... :)

Susan

Re: Fishy Teeth

By the way, chance + time + random mutations clearly doesn't encapsulate evolution. For instance, it doesn't include pressures from competition. 

-b

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Re: Fishy Teeth

Hey Susan,

Thank you for pointing out all the uses of evolution in the article. This makes my point easier to state. 

My original point was this: the facts of the vast theory of evolution have helped scientists make important new discoveries.

And I gave an example.  This is the new discovery: "The researchers say their finding introduces into the scientific literature a core evolutionary list of molecular pieces needed to make a tooth." And all the things that you pointed out helped the scientists get to this discovery.

You can say that they were wrong every step of the way, but wouldn't that make their results, more than likely, wrong? This is why I say evolution is predictive. By following the evolution to it's logical conclusions, one finds new and true discoveries. Just as with math, evolution has an "unreasonable" propensity for predicting things correctly. 

Another way of seeing how helpful evolution is in science is this: scientists are egotistical. If the evolutionary biologist didn't actually help the geneticist in any useful way, do you think he would let them put their name on his paper? But he did. 

As for specified complexity, surely it exists. But it is not part of the theory of evolution. And it is unnecessary when explaining biological form and function (unless we're talking biological engineering). Dawkins explained this over and over. Did you not grasp it?

-b

   

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Re: Fishy Teeth

Surely you can hear my eyes rolling from thousands of miles away. 

I gave you a specific example of evolutionary biologists helping a geneticist ferret out a modern scientific result, and you fire back that some scientist used God's organizational prowess to find new elements. Can you not see the difference?

And you think it was a LACK of christians that kept us from making scientific breakthroughs?! That's a laugh!

Back to complexity. This idea of specified complexity is silly. You have to believe in intelligent design to believe that an organism has specified complexity. 

I'd say more, but my thumbs are tired. 

-b

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I was right

Nano balls: http://pubs.acs.org/doi/abs/10.1021/mp060107e

Hamster generators: http://www.technologyreview.com/energy/22103/

Fishy Teeth

Hey Susan,

Here's another article:

http://www.nidcr.nih.gov/Research/ResearchResults/InterviewsOHR/Cichlids.htm

This one is a good example of what can be accomplished by geneticists when they have evolutionary biologists on-hand to help out. Evolution not only is a neat and tidy explanation for the origins of all life on earth, it is predictive and useful for propelling science forward. Young earth creationism is none of these things.

-Brandon