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

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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

Sent from my iPhone

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

Sent from my iPhone

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

Sent from my iPhone

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

Simple Robots

Hey Susan,

This is only tangentially related to evolution, but our conversations have made me think about something. I've been reading about invasive species and such, and I was thinking that it would be nice to have a way of getting rid of them. But there's a reason they're invasive, right? They have no natural predators, or they compete better than whatever's filling that local biological niche. So it's hard to git em. 

Well, I mentioned to my friend Ben that we should just make robots that go out and kill the buggers we don't like. He was immediately dismissive. I was taken aback my his assuredness, and so I asked why he thought that. He said that we can barely get a "roomba" (irobot.com) to work. And that was the sum total of his answer. 

Of course, I hadn't been thinking of a roomba, or a Terminator (http://www.imdb.com/title/tt0088247/) -stlye humanoid gun-toting machine. I don't know, I was thinking more of a ball that moves around. Like a hamster ball (http://www.youtube.com/watch?v=98M1mqKGJJc) without the hamster. Hell, it could even have a hamster making it move. The goal is to kill the thing to be killed, not to be cute or cool while doing it, and certainly not to be clever while doing it. 

Let's say you want to get rid of squirrels: let loose a bunch of rolling things that roll around until they bump into the squirrel. There needs to be a way to positively identify the squirrel, and then you kill the offending animal some way. Poisoned food, injections, explosions, entrapment...something. Boom! No squirrel. 

Ok, there are lots of logistical problems with this. But here comes the fun part: trying (and failing) to solve one problem sometimes presents a whole new line of reasoning. So this is it: a different way to make a robot. An evolutionary robot. 

Maybe the reason that we've had such a hard time making robots is that we've been trying to make mammal-like robots. Robots that move around on two or four legs (on wheels or not), making carefully calibrated movements to get from point A to point B and then accomplish it's tasks. But that's hard! As any evolutionary scientist will tell you, it takes a long time to get that kind of precision down. It took the earth 4 billion years, for gosh sake! Man is clearly speeding up the process, but we're failing miserably at the same time.

So why don't we start simple? Like in the rolling ball scenario?

Jon (who is a huge instigator of biological inquiry in my life) was telling me about some single-celled organisms. Probably bacteria. These things are so dumb! Basically a ball with a tail this guy will spin its tail clockwise, which propels it forward. After a short while the guy stops and "tastes" its surroundings to see if the amount of food in the area has increased or decreased. If it has increased, he spins his tail clockwise again and continues in the same direction. If, on the other hand, the food supply has decreased, he spins his tail counter-clockwise, which has the effect of rotating the creature crazily, making it point in a different direction. And then it spins its tail the clockwise again to head off in this new direction.

In this way, using simple randomness and probability, the creature gets enough food to survive and reproduce.

I love the simpleness and stupidity of this thing. It's not the most efficient way of getting to food. Many wrong turns are made. But it gets the job done! 

Even if my idea of making a swimming robot that is nothing but a ball with a tail (and maybe a deadly hypodermic needle) isn't actually going to manage to kill off an invasive fish species, it's an interesting idea for future problems that might be solved by simple, stupid machines. 

I just thought of one! Send one to Mars! I mean, that rover is so meticulous and slow, and ground control cheers whenever it hurdles over a pebble. If they sent along 3,000 randomly rolling balls with cameras, they'd perhaps get to see more of the planet. And take more risks. Maybe they could have a clear plastic shell for protection with solar panels with apertures for cameras just underneath. They could beam their info to the rover, which could beam it up to earth.

In fact, they could have a different ball for each thing they were trying to accomplish. A ball for testing dirt samples. A ball for sensing air quality. An explosive ball that sends info about buried minerals back to the rover right before it succumbs to immolation.

As an aside, I've heard people theorize about "nano-robots" that we'd place in our blood to find and destroy diseases. I can only imagine that these guys would be much more like my robots than like Johnny 5 ( tinyurl.com/29oagz4 ) . 

That's all I got,

Brandon

PS I guess this is what happens when I'm typing with all ten of my fingers instead of just my thumbs!

Re: this would be huge medical news

Hey Brandon,

You’re right—this is a touching, in depth, and fascinating article.  Schizophrenia has caused a lot of pain for a lot of people, and it’s encouraging to hear of people researching to find remedies.

In the past few years, geneticists have pieced together an account of how Perron’s retrovirus entered our DNA. Sixty million years ago, a lemurlike animal—an early ancestor of humans and monkeys—contracted an infection. It may not have made the lemur ill, but the retrovirus spread into the animal’s testes (or perhaps its ovaries), and once there, it struck the jackpot: It slipped inside one of the rare germ line cells that produce sperm and eggs. When the lemur reproduced, that retrovirus rode into the next generation aboard the lucky sperm and then moved on from generation to generation, nestled in the DNA.

This account is based on evolutionary theory, as if the theory were fact.  There are other possibilities.  What is being described as a retrovirus, may simply be a strand of  non-coding DNA which serves a specific function in both humans and monkeys, just as a certain engine part may be used in both a lawnmower and a weed-eater.  What happened six thousand, or sixty million, years ago cannot be observed, so the geneticists’ account can be based only on their interpretation of forensic evidence

Sabunciyan has found that an unexpectedly large amount of the RNA produced in the brain—about 5 percent—comes from seemingly “junk” DNA, which includes endogenous retroviruses...

Here, the assumption is that endogenous retroviruses are a part of ‘junk’ DNA.  Yet ‘junk’ DNA is being discovered to have specific, necessary, and very important roles in body function. The article itself even recognizes that all ‘junk’ DNA isn’t really junk.  It is very likely that there is no such thing as ‘junk’ DNA.  If that is true, these ‘endogenous retroviruses’ may simply be  normal DNA components that have always been present.  And these normal components can be damaged by mutations, which are known to be almost always negative.  In this case Perron’s retrovirus may simply be a section of normal DNA which is sometimes damaged in some way, thus predisposing a person to disease.

As far as schizophrenia itself, as well as other mental disorders, one cannot say it has a simple cause—there are both nature and nurture components. Since the article states that all people carry the retrovirus for Schizophrenia, there must be other factors which explain why some people get sick and others don’t. The article focuses on biological factors such as illness and strength of one’s immune system.  Early trauma in general, whether it’s from disease, abuse, or natural disasters, can trigger emotional disorders.  While problems such as schizophrenia and Bipolar Disorder occur even in high functioning, emotionally healthy families, the rates of occurrence are higher in chaotic, dysfunctional families.  So what you have are a bunch of factors working together—if none are present, illness isn’t likely (but still possible), but if  many factors are present (illness, trauma, family dysfunction, poor immune system, other yet unknown factors), the odds of getting sick are much greater.  In the story of the twins at the beginning of the article, one twin was physically healthy at birth, while the other was ill and may have been born with a poorer immune system (the article doesn’t say).  In addition, the ill twin had to stay in the hospital for a month—it’s quite likely that this twin didn’t get the nurturing and loving physical contact that the healthy twin at home did—this would be an additional emotional trauma for the child, possibly leading to attachment issues.  It could also be that the Perron’s retrovirus (or normal DNA component, depending on one’s worldview) in the sick twin had been damaged in some way (while not discussed in the article, it could be a subject of future research).  So, the factors add up, making the sick twin much more likely to experience Schizophrenia or some other mental disorder.

Overall, based on this article, I’d say the research is probably valid, but the evolutionary assumptions are not.  One doesn’t have to know where this strand of DNA (Perron’s retrovirus) came from in order to study the effects it can have on people.  The researchers discovered important information, and I can see several avenues for further study and exploration.

Susan

Re: more evolution theorizing

Hey Brandon,

I’m considering a book about genetics now.  If Jon has a good suggestion, it might be helpful to look at it, too.

Going on an archeological dig actually has the potential of being a fun thing, and it would definitely give us some good face time—it’s the logistics that I’ve got to think through.  I have family and job, and there are such things as cost, timing, transportation, location to consider.  When you first suggested it, I wasn’t sure that you meant it, so didn’t think about it much.  I’ll give it more thought now.

Susan

Re: more evolution theorizing

Hey Brandon,

Okay, here goes...

Run of the mill complexity:  a garbage dump is a complex pile of junk. A bunch of random magnetic letters on a refrigerator.  NaCl forms crystals under certain conditions; these crystals are ordered and may be considered to be complex, but their ordering is repetitive, based on NaCl’s chemical properties, and has no message carrying capacity from a biological standpoint.  A flask of inorganic amino acids has complexity, but no specific function—they would have to be arranged in a certain way in order to carry the information needed to function in an organism.  (If the flask contains both R- and L-isomers, the amino acids couldn’t  form the needed arrangement because of the presence of the wrong isomer.  If just one molecule of the wrong isomer joined to a DNA strand, it would keep the strand from  forming the double helix shape, and it wouldn’t function properly.)  A building supply or auto parts store has run of the mill complexity—there are a lot of parts or building blocks, but they don’t do anything on their own. (of course, individual items in a store might have specified complexity, such as a shower head or an AC unit, but there is no specification as to how these individual units are to fit into a larger unit such as a building)  

Specified complexity:  A jet plane is full of specified complexity; its parts have been created and specified to fit precisely with each other in order to function properly.  The machinery used to create those parts have been precisely calibrated in order to meet the necessary specifications. Human technology, such as circuit boards and computer software, exhibit specified complexity. DNA has specified complexity; specific amino acids are arranged in very specific manners so that the DNA’s codons can direct specific functions in an organism.  Without the correct ingredients and arrangement, one has only a complex mass of chemicals (run of the mill complexity) that perform no function at all.  DNA codes specify for the creation of the enzymes, hormones, and other processes needed for body function.  Consider the Kreb’s cycle of metabolism—it consists of a number of steps, each with its own specific enzyme which must be created according to the ‘blueprint’ found in the organism’s DNA.  A bunch of letters on the refrigerator spelling a message (“See you tonight”) has specified complexity.  One could say that when complexity is specified, it is organized in a way that produces a certain action or carries a certain message.  Each codon in DNA has a purpose, whether it’s to produce a certain eye color, build a certain enzyme, or moderate a specific cellular function.

I’m thinking there’s a proper name for ‘run of the mill’ complexity, but it’s not coming to my mind.

Specificity has to do with function, not goals.  Biological organisms function in very specific ways.  They have cells and body parts that function in specific ways which are useful to the organism.  The purpose of the eye is to see one’s surroundings and communicate that info to the brain.  Nerves, muscles, neurons, blood vessels, and so on work together so that the eye can perform its proper function.  These muscles, neurons, and so on, are made up of cells, which themselves are made up of even smaller parts, such as mitochondria, nuclei, and cell walls.  At each level, the parts must operate within certain specified parameters in order for the total organism to function properly and stay alive.  If your body pH varies outside a very narrow range, you die.  If your pancreas doesn’t function properly, you have diabetes.  

What you appear to be saying is that one can get from run of the mill complexity to the very specific complexity present in living organisms, simply by random processes and enough time, with no intelligent intervention.  Yet no one has ever observed specified complexity developing through random processes over time.  Planes and computers don’t build themselves, and letters don’t form into words of their own volition.  In each case of specified complexity, an outside intelligence acts in order to produce it—engineers design and build airplanes, experts design and build computers and circuit boards, a family member creates a message on the fridge, an author writes a book. Even the ‘cyber creatures’ in that article wouldn’t have existed without the intelligent input of computer scientists and programmers.  It would seem logical to conclude that an intelligent being (I would say, the God of the Bible) also created the universe and the living beings that exist in it.

Susan

Fwd: this would be huge medical news

This is such an amazing article! It's touching, well-written, in-depth, and fascinating. It even touches on how evolutionary theory is being used to make modern medicine and push at  the edges of biology (and evolution is a pet interest of mine lately). But mainly it brings us up to date on research in degenerative brain diseases and psychoses in an extremely understandable manner. And that research is so exciting! And not a little bit scary. 

Mom, Dad, did I ever have an infection when I was just born? I really hope not:)

Love,

Brandon

PS Thanks for the story, Ben!

Sent from my iPhone

Begin forwarded message:

From: Ben 
Date: December 1, 2010 2:37:27 PM PST
To: Brandon 
Subject: this would be huge medical news

evolution connection on page 3:
http://discovermagazine.com/2010/jun/03-the-insanity-virus

Evolution of Relationships

Hey Susan,

If you want to hear some very shocking stuff, listen to episode 210 of the Savage Love Podcast which is a audio sex advice column that is hosted by Dan Savage, a gay man and fierce advocate for gay rights. He recently also launched the "It Gets Better" Project wherein people ( including Obama and Sec. Clinton) post videos letting suicidal gay kids know that it will get better.

In the episode in question, Savage interviews an author on his book about the evolutionary origins of human sex.

Here's the link:

http://podcasts.thestranger.com/

Go to and listen to episode 210.

Warning! It's very crass with curse words and explicit talk of sex.

-Brandon

Fwd: cross-species gene mapping as computer game

How fun!

Sent from my iPhone

Begin forwarded message:

From: ben
Date: November 30, 2010 1:28:54 PM PST
To: Brandon 
Subject: cross-species gene mapping as computer game

http://www.wired.com/wiredscience/2010/11/phylo-game/

Re: more evolution theorizing

And what ever happened to my idea about us learning about genetics? You'd probably tear it up with your background in biology, but I'd probably struggle along until I learned a thing or two. Do you want me to ask Jon for a good book? 

And what about us visiting a archeological dig? I thought you'd eat that up. It'd get you out of the knobs and give us some face time. 

-b

Re: more evolution theorizing

Hey Susan,

I'll try to be open minded about "specified" complexity, though I have an inclination not to be. I don't understand your definition. The theory of evolution doesn't claim that natural selection leads to a "specific" goal. In fact, as Dawkins says, everything is intermediate. So I don't know why you'd even need an idea of "specified" complexity when talking about evolution. 

Can you give me examples of "specified" complexity? And how bout some "run of the mill" complexity examples? I'm not sure I know what you mean by that either. What do you mean by complexity having a purpose? Or usefulness? Those two words can be pretty arbitrary. And most everything carries information. Change the direction of one atom, and you can store information (in fact, don't they do that already?). 

I think I'll stick to this and let my original comments about simple systems becoming more complex be my response to your attack on a "central tenet" of evolution. 

-Brandon

Re: more evolution theorizing

Hey Brandon,

Yes, we may be a little at cross purposes here.  Yes, there can be increased complexity in spite of entropy in the short term, in the right conditions.  However, I’m focusing on specified complexity, complexity with a purpose, usefulness, complexity which carries information, the kind of specified complexity that occurs only in living organisms (think of the specific DNA which codes for the production of a specific enzyme needed for a specific metabolic process in a cell).  Apparently I haven’t done a good job at explaining my thoughts clearly.  I apologize.  Sure you can get your basic run of the mill complexity, given the right conditions, but as far as I know, one does not find specified complexity without intelligent input somewhere along the line.  Even with intelligent input to allow the development of specified complexity, that information is eventually going to break down because of entropy, barring further input from a source of intelligence.  For example, new cars eventually wear out and break down, although the process can be slowed by the intelligent actions of a mechanic.  Because of entropy, a car isn’t going to morph into something better and more complex on its own.  

I give an example that refutes one of your claims, and you respond by pointing out I have not managed to defend every last argument of the vast theory of evolution

I responded to the article as a whole, not just to the part about increased complexity—I didn’t realize that you wanted only to focus on that one area.  As far as every last argument about the theory of evolution, one of the basic tenets of Darwinian evolution is that it occurred on its own without input from any intelligence.  The article discussed a software program which led to increased complexity.  I simply made the point that it required intelligent input in order to create the computers and software which produced these digital beings.  That is not irrelevant, as it pertains to that basic tenet.  It’s not “every last argument”, but one of the major tenets of the theory of evolution.

It’s always good to hear your responses—that’s the only way I can know if what you’re hearing matches what I’m trying to say. :)

Susan

Susan,

 

You are pulling an old trick that you are fond of. I give an example that refutes one of your claims, and you respond by pointing out I have not managed to defend every last argument of the vast theory of evolution. I pointed out that these programs that show increasing complexity based on simple rules goes against your wrong conception of entropy. That is all I claimed.

 

As for your response to my point about entropy, I agree with everything you said. But you did not mention the point that you are wrong about. The point that you are wrong about is that you believe due to entropy, increasing complexity cannot happen. At least this is what you used to believe. Perhaps you've since modified your stance.

 

If your new stance is: "complexity can happen spontaneously, but complexity cannot happen to the extent that you see on earth," then that is an argument that we can discuss, but you should at least lay it down as such.

 

Once again, I think our discussion about evolution is boiling down to: to what extent is something possible? For instance, to what extent is adaptation possible? We agree that adaptation happens, but can a land mammal adapt its way to becoming a sea mammal? For instance, to what extent can entropy be overcome? We both agree that spontaneous short-term complexity can occur in spite of entropy (right?), but what do we mean by "short-term" and "complexity"? And can complexity occur long enough for a land mammal to adapt to be a sea mammal?

 

You see? They're the same problem! Do you agree?

 

Yours,

Brandon

On Tue, Nov 30, 2010 at 10:00 AM, Susan  wrote:

Hey Brandon,

The Wired article on digital creatures doesn't support Darwinian evolution as much as you might think.  Darwinian evolution requires that living organisms develop from non-living substances, and then increase in complexity, with no input or direction from a higher intelligence. The computer didn't create itself.  The original software didn't create itself.  The very existence of the computer and original software required intelligence—without the input of intelligent, creative human beings, there could be no computers, no software with the ability to develop the 'digital creatures' in the first place.  

The article also wasn't clear about what kind of complexity the program was developing.  In living organisms, there is specified complexity—specific genes/enzymes have specific functions—amino acids are arranged in such a way that they carry specific information to do a specific job.  In these digital creatures, what is the function of the increasingly complex codes that are developed?  Do they serve specific purposes?  Do their flashes actually mean something?

As far as entropy, it is in force in all systems, open or closed.  There is really no such thing as a truly isolated system.  The fact that the earth receives energy from the sun does not mean that entropy never occurs on the earth.  

Susan

Re: more evolution theorizing

Hey Brandon,

The Wired article on digital creatures doesn’t support Darwinian evolution as much as you might think.  Darwinian evolution requires that living organisms develop from non-living substances, and then increase in complexity, with no input or direction from a higher intelligence. The computer didn’t create itself.  The original software didn’t create itself.  The very existence of the computer and original software required intelligence—without the input of intelligent, creative human beings, there could be no computers, no software with the ability to develop the ‘digital creatures’ in the first place.  

The article also wasn’t clear about what kind of complexity the program was developing.  In living organisms, there is specified complexity—specific genes/enzymes have specific functions—amino acids are arranged in such a way that they carry specific information to do a specific job.  In these digital creatures, what is the function of the increasingly complex codes that are developed?  Do they serve specific purposes?  Do their flashes actually mean something?

As far as entropy, it is in force in all systems, open or closed.  There is really no such thing as a truly isolated system.  The fact that the earth receives energy from the sun does not mean that entropy never occurs on the earth.  

Susan

Re: The Top Ten Daily Consequences of Having Evolved | Science & Nature | Smithsonian Magazine

Hey Brandon,

I read the article.  It assumes Darwinian evolution is fact, then explains a number of phenomenon according to that assumption.  Where are the scientific studies on which these explanations are based?  I remember very well being taught  in school that the appendix was a vestigial organ, a product of evolution which was no longer necessary. Scientists now recognize that this belief was wrong.  Same for the thymus and tonsils.  “Junk” DNA isn’t junk, but contains information necessary for cell function.  Consider the article’s statement about the need to pull wisdom teeth—some dentists question whether it should be done routinely simply based on the (evolutionary) idea that because human jaws and brains have evolved, wisdom teeth are no longer needed. Other dentists believe that such things as diet  and growth rates may be the primary causes of why human mouths seem to be smaller.  For example, people now tend to eat more cooked, soft foods than hundreds of years ago, so do less chewing—the if-you-don’t-use-it-you’ll-lose-it principle.  And Americans, who tend to have more problems with small mouths, also may be maturing faster than people in other parts of the world due to hormones in food; as a result facial bones may not have enough growth time before wisdom teeth come in.  And of course, there’s the possibility of genetic entropy occurring, in which the human population would lose, over time, the genetic information needed to make jawbones grow enough to make space for all the teeth.  So, for just this one phenomenon there are a number of very probable causes other than Darwinian evolution.  It’s silly to assume that this, or anything else listed in the article, is simply a consequence of Darwinian evolution and nothing else.

And, if evolution did lead to smaller jaws and fewer teeth, this would seem to indicate a loss of complexity, rather than a gain.  How does that support Darwinian evolution?

Susan

Fwd: more evolution theorizing

Hey Susan,

 

The article below gives an example of simple things becoming more complex or organized over time over time. There are many examples of computer programs that do this. Given a series of functioning computers and enough electricity, this type of "automatic complexification" could continue ad infinitum. This of course goes against your idea of how entropy works. The "outside force" that allows entropy to be outdone in this case would be electricity and replacement computers. The "outside force" propelling complexity on the earth in spite of entropy is the energy from the sun.

 

-Brandon

---------- Forwarded message ----------
From: Ben Date: Mon, Nov 29, 2010 at 1:07 PM
Subject: more evolution theorizing
To: Brandon

 

http://www.wired.com/wiredscience/2010/11/digital-organism-evolution/

Re: The Top Ten Daily Consequences of Having Evolved | Science & Nature | Smithsonian Magazine

Very nice article, Ben.

-Brandon

Sent from my iPhone

On Nov 28, 2010, at 11:51 PM, Ben wrote:

> http://www.smithsonianmag.com/science-nature/The-Top-Ten-Daily-Consequences-of-Having-Evolved.html?device=iphone&c=y

Re: The Tuatara, a Still-Evolving Original - NYTimes.com

Hey Brandon,

Can’t quite figure out what this article is trying to say.  It describes the traits of the tuatara—straightforward and factual.  

It also asserts that “ a few regions of tuatara DNA appear to be evolving at hyperspeed <http://www.cell.com/trends/genetics/abstract/S0168-9525%2808%2900003-6> , possibly the fastest mutation rate yet clocked in a vertebrate genome.”  And, “The quick-changing sequences are limited to so-called neutral regions of the tuatara’s DNA, affecting filler codes, rather than the molecular blueprints for how to build a tuatara.”  This is where things get a little vague and nonspecific.  What do they mean by evolving at hyperspeed?  What are neutral regions?  It almost sounds as if they’re referring to ‘junk’ DNA.  And, since the tuatara hasn’t changed for ‘hundreds of millions of years’, what would be the evolutionary significance of  these regions evolving at hyperspeed?  The creatures are still tuataras.  Are the authors trying to imply that the tuatara is getting ready to evolve into a higher, more complex kind of organism?  Do the authors see the mutations as being good or deleterious?  

Unfortunately, I don’t have easy access to the full study linked to in the NYT article—perhaps it would answer some of my questions. The NYT article itself doesn’t seem to be much more than an interesting description of an unusual animal, with an obligatory reference to evolution thrown in.

http://jvi.asm.org/cgi/content/abstract/81/23/12979
This study found no beneficial mutations at all.

http://www.nature.com/nature/journal/v467/n7315/abs/nature09352.html
Study of fruit flies over 600+ generations finds a resistance to change.  The fruit flies remained fruit flies.

Susan

The Tuatara, a Still-Evolving Original - NYTimes.com

Why haven't we made little robots that kill unwanted animal and plant species yet?

-b

http://www.nytimes.com/2010/11/23/science/23angier.html?pagewanted=2&_r=1&src=fbmain

Fwd: only slightly creepy biology

From: Ben
Date: November 10, 2010 2:12:18 PM PST
To: Brandon
Subject: only slightly creepy biology

http://arstechnica.com/science/news/2010/11/an-array-of-body-neurons-helps-larvae-see-light.ars

Loss of amphibian population

Hey Brandon,

Neither the fish in the Royal Society article nor the development of bacterial resistance support Darwinian evolution—they’re both examples of adaptation to environmental conditions.  For example, some bacteria carry latent genes that code for antibiotic resistance; these genes become active in the presence of certain antibiotics.  In other bacteria, mutations lead to resistance to certain types of antibiotic, but the resistance comes with a cost, such as slower growth rate or decreased resistance to other antibiotics—when these bacteria are in natural conditions (with no antibiotics), they aren’t able to compete with the faster growing non-mutated bacteria.   

Here are several related articles...  

The agents of divergent selection are extrinsic and can include abiotic and biotic factors such as food resources, climate, habitat, and interspecies interactions such as disease, competition, and behavioral interference.

This comes from Evidence for Ecological Speciation and Its Alternative, Dolph Schluter, in Science Magazine ( http://www.sciencemag.org/cgi/content/full/323/5915/737?ijkey=57JzKGxEe.F.Q&keytype=ref&siteid=sci ).  This sounds good when you’re promoting Darwinian evolution.

Potential causes [of worldwide decrease in amphibian population] include habitat degradation, pollution, acid rain, ultraviolet irradiation, pesticides, predators, competition from introduced species, climate changes, and disease.

From Holt, W. V. et al, eds. 2003. Reproductive Science and Integrated Conservation. Cambridge, UK: Cambridge University Press, 360.  (You can look this page up online at amazon.com.)  This sounds good when you’re talking about protecting the environment.

So, what we have here are scientists with very different perspectives based on different fields of study.   One says that climate, habitat, and so on, drive evolutionary change and development of new species and classes of organisms, and Dawkins would agree with this.  The other suggests that these same factors lead to population degradation and loss of many  species.  Apparently the factors that are said to have driven Darwinian evolution (with its development of increasingly complex species) in the past, and supposedly continue to do so now, also lead to species degeneration and loss.  How do the same factors manage to lead to both increase and decrease of species (and concomitant  genetic information)?

According to the second reference, a decrease in amphibian population over time has been observed by scientists—that part is something we can know for sure.  What isn’t known for sure is the cause for the decrease in population.  It doesn’t make sense that the same factors would drive both the increase of complexity/genetic information and the decrease of complexity/genetic information.  If climate, habitat, and so on do drive Darwinian evolution, why are amphibians not evolving into something else rather than disappearing?  

As previously reported from allozyme analyses, A. japonicus exhibits little genetic differentiation, in strong contrast to salamanders of the genus Hynobius with which their distributions overlap. This reduced genetic variability in A. japonicus is attributable to a unique mating system of polygyny, delayed sexual maturity, notable longevity, life in a stable aquatic environment, and gigantism, as well as bottleneck effects following habitat fragmentation and extinction of local populations during Quaternary glaciations. The species is thus susceptible to extinction by potential environmental fluctuations, and requires extensive conservation measures. Matsui, M., et al. 2008. Reduced genetic variation in the Japanese giant salamander, Andrias japonicas (Amphibia: Caudata). Molecular Phylogenetics and Evolution. 49 (1): 318-326. linkinghub.elsevier.com/retrieve/pii/S1055790308003795

According to this study, A. japonicus (the Japanese giant salamander) has reduced genetic variability (genetic differentiation).  Organisms that have insufficient genetic variability are less able to adapt to environmental changes.  Because of this, the giant salamander is susceptible to extinction due to environmental fluctuations. This reduced genetic differentiation would be expected with genetic entropy.  If Darwinian evolution were taking place, one would expect environmental fluctuations to be driving further evolutionary development of new genetic information in order to help the amphibians adapt—but this doesn’t seem to be taking place.  Overall, we readily observe extinctions, but no one has ever observed the development of life from non-life or of a new class of organism with greater complexity from one with lesser complexity, such as a eukaryote from bacteria.  We readily observe adaptations within a kind, such as the above bacteria and fish, but we don’t observe one kind developing into another, more complex kind.  

Susan

Fwd: evolution article

From: ben
Date: November 8, 2010 1:13:30 PM PST
To: Brandon Meredith <mathcadd@gmail.com>
Subject: evolution article

A cool example of artificial selection, kind of like antibiotic resistant bacteria, but on an animal:
http://rsbl.royalsocietypublishing.org/content/early/2010/09/06/rsbl.2010.0663.full?sid=b26a2194-7a63-4bfc-acdd-b62460fffa9a

Re: Evolving altitude aptitude

Hey Brandon,

Well, it would make sense for either Adam or Eve to have carried this particular gene, although it doesn’t mean that the gene was necessarily active in either one of them. People carry the genes for many different traits which they don’t have themselves.  Even though I have green eyes, I probably carry the genes for blue, brown, and/or other eye colors.   I’ve seen families with red-headed kids who whose closest red-headed relatives were several generations back.  Adam and Eve would have had the genetic material for all the possible traits, and then various populations, as they spread out and became more isolated, would have lost some traits because of less genetic material available to pull from.

I do find it much more logical and scientifically sound to believe that a Creator God created everything than to believe that living organisms came from non-living material, then developed complex genetic information through mutation and natural selection, and without any intelligent guidance.  I suppose this will continue to be a bone of contention for us.  Perhaps you could find research showing how Darwinian evolution handles handedness, entropy, and the other problems I’ve mentioned?  

Also, if I could find one stretch of human DNA that had three beneficial configurations, wouldn't that disprove your logic?  

I’m not sure what you’re trying to say here—perhaps you could rephrase?

Susan

Fwd: Evolving altitude aptitude

Hey Susan,

I absolutely detest having to talk about what you base your ideas on, but I see no way around it in this case. You say that this special stretch of DNA in the Tibetans has always been around, presumably placed there by a god for the precise reason of making a happy population on a mountain  but if you also believe that all of humankind came from one man and one woman, then you believe that either Adam or Eve had this special stretch of DNA that the Tibetans now have. Is that what you really believe?

Also, if I could find one stretch of human DNA that had three beneficial configurations, wouldn't that disprove your logic?

-Brandon

Re: Evolving altitude aptitude

Hey Brandon,

Yep, I’d say that both articles present very good examples of adaptation, not of Darwinian evolution, since in both cases, there was no change in the basic organism—the frogs were still frogs, and the people were still people.  Both the frogs and the humans adapted to their environment by using genetic information already present in a portion of the population.  In both studies, the assumption is that there was a mutation at some point, yet we already know that most mutations are harmful or, at best, almost neutral (or barely harmful).  In neither article is there proof that a mutation actually occurred—it is assumed to have occurred because the scientists were working from an evolutionary perspective.  What is known is that information in DNA allowed the frog and human populations to adapt to their environments—that information kicked in when needed in order for the population to adapt.  

The Berkeley article talked about gene variation frequency of a section of DNA called EPAS1.  Scientists compared the frequency of EPAS1 in the Tibetans and in other Chinese populations, and found that the Tibetans had the highest frequency.  Note that some non-Tibetans also had this gene, although at a much lower frequency—why would this be the case if the gene were a mutation among the Tibetans?  I suppose one might say that the mutation occurred in one or two individuals before humans migrated to Tibet, but then, why would such a mutation spread to the general population when there would be no need to select for it?  If none of the earliest Tibetans had the proper variant of the EPAS1 gene which allowed them to adapt to their environment, they would have had to deal with the altitude sickness that most others experience—why would they have continued to live in such a hostile environment for the ‘hundred or so generations” it took for them to adapt?  The more likely scenario is that the proper variant was already in place (though not necessarily active, because not needed) in a good number of Chinese, and those early Tibetan settlers that had it adapted and fared better.  Over time, as the Tibetans reproduced among themselves, the frequency of the trait increased, while it stayed low elsewhere.

He explained that the faster moving toads even reproduced more quickly. But this could point to a chink in their biological armour.
"They have to be trading something off to do that," he said. "And one of the things we suspect is that they're trading off their immune systems."

It was interesting to note that the researchers expected the ‘good’ mutation leading to faster movement would be accompanied by something negative (suspected lower immunity).  This goes along with what I’ve said before—that most mutations are negative, and when ‘good’ mutations are selected/activated, they will be accompanied by ‘bad’ ones, as selection is by phenotype and not genotype—one cannot select for ‘good’ traits only.  In truth, neither individual organisms nor nature actively selects anything.  Individuals live or die based on individual ability to adapt and on other environmental factors (war, sickness, natural disasters,  getting eaten by another animal, etc.), but they can’t choose which traits to pass on to the next generation.  Individuals with good traits could get eaten or die of sickness before producing offspring, while individuals with maladaptive traits might produce offspring before dying—either way, having a certain trait doesn’t guarantee that it will be passed on.

Susan

Fwd: Evolving altitude aptitude

From: Brandon
Date: Thu, Oct 21, 2010 at 10:29 AM
Subject: Fwd: Evolving altitude aptitude
To: Susan


I've sent u an article about the Tibetans before, but this one is much more in depth. Also, it's an example of an adaptation at the molecular level due to a mutation in DNA that is beneficial to the Tibetans. They even know which stretch of DNA does it. Again, this is natural selection (which naturally involves slight mutations with every generation) / evolution at work.

-b

---------- Forwarded message ----------
From: Ben
Date: Mon, Oct 18, 2010 at 2:54 PM
Subject: Evolving altitude aptitude
To: Brandon


http://evolution.berkeley.edu/evolibrary/news/101001_altitude

Fwd: another evolution article

From: Ben
Date: Tue, Oct 19, 2010 at 10:29 AM
To: Brandon

sorry for the glut of articles lately.  lots of science happening, i guess
http://news.bbc.co.uk/earth/hi/earth_news/newsid_9096000/9096795.stm

----------
From: Brandon
Date: Thu, Oct 21, 2010 at 10:23 AM
To: Susan


I know that you're going to say that it's natural selection and not evolution, but this author clearly doesn't see a distinction between the two (and neither does Dawkins).

-b

Re: How Plants Drove First Animals Onto Land

Hey Brandon,

Well, I suppose that since you’ve returned to our evolution/creation discussion, you must be feeling less stressed.  If that’s true, I’m glad. :)  And hopefully it means that either some stressors have gone away or you’ve found good ways to manage the stress.

Now to the article...  I don’t know what to think, and I’m not sure what you want me to get from it—it appears to me that the researchers took some data about molybdenum and oxygen concentrations, then built a story around it to fit evolutionary ideas.  At least the author first admitted the uncertainty of the models for the distant past before making his assertions about the meaning of the data.

According to another article (http://live.psu.edu/story/38514), researchers at Penn State have found that there was as much atmospheric O2  three and a half billion years ago as there is now, as evidenced by the presence of O2 in the very deepest of rocks sampled—very different from what is claimed in the article you just sent.   See also http://www.nature.com/ngeo/journal/v2/n4/abs/ngeo465.html .  In your article, precursors to plants evolved 400-550 million years ago.  According to the Penn State article, plants or their precursors must have been around 3.5 billion years ago.  If both atmospheric O2 and plants (or their precursors) have been around almost since the beginning, why could not other plants and animals have been around since then, too?  (By the way, the Penn State study stated a conclusion based on what is already known about chemistry and geology.  Your article stated a conclusion, about plants driving first animals onto land, based on evolutionary theory.  Therefore, I think the Penn State study has a higher value.)

The Penn State findings fit well with Biblical creation theory, as it is consistent with the idea that the earth was livable and had plants on it almost from the beginning.  Of course, I disagree with the dating in all the articles, as I’m a young earth proponent and question the millions and billions of years—but that’s for another discussion. :o)

Susan