Monday, December 27, 2010

Re: Genetics Book

Re: Genetics Book Hey Brandon,

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

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

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

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

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

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

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

Take care,

Susan

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

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

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

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

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

Susan

Sunday, December 26, 2010

Re: Genetics Book

Hey Susan,

I.

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

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

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

II.

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

III.

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

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

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

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

IV.

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

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

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

V.

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

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

VI.

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

Thanks,
Brandon

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

Hey Brandon,

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

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

Hope you've had a wonderful Christmas weekend!

Susan

Saturday, December 25, 2010

Genetics Book

Hey Susan,

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

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

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

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

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

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

Later,
Brandon


Friday, December 24, 2010

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

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

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

-b

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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

Friday, December 10, 2010

On studying the opposition

On studying the opposition Hey Brandon,

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

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

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

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

Susan

Thursday, December 9, 2010

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


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Re: Fishy Teeth

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

Tuesday, December 7, 2010

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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Monday, December 6, 2010

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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Sunday, December 5, 2010

Saturday, December 4, 2010

Fishy Teeth

Hey Susan,

Here's another article:


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!

Thursday, December 2, 2010

Re: this would be huge medical news

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

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

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

Wednesday, December 1, 2010

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 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


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