Da Vinci and Wikipedia

Hey Susan,

I was pretty excited to find this nuggett from wikipedia. On the webpage devoted to fossils, the attribute this quote to Da Vinci where he argues against the idea that the biblical flood placed shells found on mountains there:

 

"If the Deluge had carried the shells for distances of three and four hundred miles from the sea it would have carried them mixed with various other natural objects all heaped up together; but even at such distances from the sea we see the oysters all together and also the shellfish and the cuttlefish and all the other shells which congregate together, found all together dead; and the solitary shells are found apart from one another as we see them every day on the sea-shores.

And we find oysters together in very large families, among which some may be seen with their shells still joined together, indicating that they were left there by the sea and that they were still living when the strait of Gibraltar was cut through. In the mountains of Parma and Piacenza multitudes of shells and corals with holes may be seen still sticking to the rocks..."^[10]

I think it's pretty fascinating that people were having arguments this lucid and heretical that long ago during a time when religion ruled the land. You go, Da Vinci!

-Brandon

Fwd: psychology of science vs beliefs

Hey Susan,

I was sent this article about science conflicting with belief, which is interesting when you take belief to mean religious faith, but equally interesting when you take it to mean deeply held ideas. Honestly, I see both of us using these justification techniques. 

-Brandon

Sent from my iPhone

Begin forwarded message:

From: Ben
Date: May 28, 2010 10:19:26 AM PDT
To: Brandon Meredith
Subject: psychology of science vs beliefs

http://arstechnica.com/science/news/2010/05/when-science-clashes-with-belief-make-science-impotent.ars

re: Junk DNA

Hey Brandon,

Very sorry you’re under the weather—hope whatever you have goes away soon...

How about giving the book another go?  Did you look at his computer program, which he talked about at the end?  Maybe the book seems boring to you because it’s written in a more scientific format, unlike Dawkins’ books, which are written more like a story.  Perhaps you can give me some specific examples of how Sanford’s arguments are contradictory?  I found his arguments to be sensible and empirically based. Reading the book does require deep concentration.

Dawkins’ books are anything but clear and concise, but that has nothing to do with the actual subject matter, other than making it more difficult to read.  Just telling me that Sanford’s book is boring, rambling, and whatever, doesn’t do much to advance our discussion, as you’re addressing the style more than the content.  If you don’t understand what he’s saying, perhaps you don’t know enough about the topic?  If so, you’re not in a position to ridicule the book.  I pointed out specific things I disagreed with in Dawkins’ books and gave specific reasons for my disagreement.  If you can do the same with this book, then we might get somewhere.

Dawkins makes the point that if evolution is false, then there should be pretty easy tests that could be performed to disprove it.

Remember, neither evolution nor creation can be proven empirically, in spite of what Dawkins seems to think.  We can only look at evidence and see if it supports our perspective.  You mentioned the distance of the stars—there’s still much to be learned about light and how it travels, and I’ve read some interesting theories that account for starlight—so, while this evidence may seem to fit more with your perspective, it’s not a proof for the long time needed for evolution.  I mentioned the faulty K-Ar method of dating rocks, resulting in rocks (including the lava cap on Mt. St. Helens) being dated at much older ages than they really are.  After accounting for excess Ar in volcanic rock, adjusted dates are more in line with a young earth.  

I also mentioned some other evidences of a young earth: presence of C14 in deepest geologic layers (should have disappeared long before billions of years), thickness of mud in bottom of ocean (should be much thicker if old earth), presence of DNA in fossils (should not be there in fossils older than a few thousand years), amount of salt in the oceans (should be much higher if earth billions of years old). I’ve also read that the earth’s orbit would have deteriorated to the point that the earth was no longer in the ‘zone’ it has to be in in order for life to exist on earth long before the billions of years needed for evolution to occur.  How would Darwinian evolution explain each of these?  Each of these facts, especially when combined, seem to me to provide strong evidence against Darwinian evolution, which requires billions of years in order to work.

Take the presence of DNA in fossils.  When that was discovered, evolutionary scientists might have worked on developing a new hypothesis about how DNA could last for millions of years longer than scientists had thought possible.  Scientists working from a creationist perspective would see the presence of DNA as evidence that the fossils weren’t as old as had been thought.  In each case the scientist is taking the same evidence—presence of DNA in fossils—and coming to different conclusions.  The trick is figuring out which interpretation comes closer to the truth.   From a biological perspective, it would be easier for me to believe that the fossils were younger than to believe that million year old fossils could still contain DNA.

And then there’s the analogy about entropy, which I gave in my first post on our blog—it would be helpful if you’d respond to that and explain how evolution fits with the analogy.  I see entropy as a strong evidence against Darwinian evolution, so it would help if you’d explain how the evolutionary position gets around this.

It would also help if you could explain how evolution accounts for the presence of handedness in organic molecules.  For evolution to occur, there must be some sort of  mechanism by which the original amino acids went from the 50-50 mixture of isomers found in non-living molecules to 100% L-isomer in order for DNA to exist and form the genes which must mutate as part of the process of evolution.  As long as there is a mixture of isomers, the amino acids might connect, but they will not be able to form the shape necessary for DNA to function as it does.  No lab has been able to  create pure isomers.  It would take a great deal of faith to believe that the random chemical processes of Darwinian evolution somehow produced the proper conditions for a mixture to go to 100% pure isomer.  What would be the probability for such a random process occurring?

By the way, scientific consensus isn’t all that important.  While it’s nice to have, consensus doesn’t guarantee that the subject of consensus is actually true.  Besides, sticking to the consensus position would tend to stifle the quest for truth.

Back to the book--

You see junk DNA as unimportant, even though Dawkins sees it as both evidence of evolution and a source of genetic material to be used in the process of evolution.  It’s natural that I would present evidence to the contrary.  If there is no junk DNA, then it can’t be evidence of evolution and can’t provide material to be used in the process of evolution.  If there is no junk DNA and all that ‘junk’ actually has specific purpose, then the random mutations that naturally occur will be interfering with the body processes guided by that ‘junk’ DNA—this doesn’t help the idea of Darwinian evolution.

Here are what I see as some of the main premises of the book:

DNA is not a simple, static, linear array of letters, but is dynamic, self-regulating, and multi-dimensional, operating on  multiple layers at once.  Each nucleotide is multifunctional, interacting with many other nucleotides.

Mutations happen at the molecular level (affecting the genotype), but selection can only be carried out on the level of the whole organism (based on phenotype).  Phenotype is affected not only by DNA but also by outside factors such as food supply.  Therefore, selecting out bad (or selecting in good) phenotypes does little to eliminate bad genotypes (or promote good ones).  

The ratio of deleterious-to-beneficial mutations has been estimated to be around one million to one.  Because most mutations are recessive, negative mutations are less likely to be selected out.  Any selection is, by definition, random.  Overall, mutations lead to a net degeneration, rather than increased complexity.

Usually there is a tight linkage between beneficial and deleterious mutations.  If one selects for a beneficial trait, one gets the deleterious one, too.  [This explains why some modern fruit trees are more productive but are also more susceptible to diseases.]

Scientists (including Kimura, who was referenced by Dawkins) agree that it isn’t possible to simultaneously select for a large number of traits due to the cost of selection.  This would mean that Darwinian evolution would have to progress very slowly indeed.  It seems that this alone would make the probability for evolution impossibly small.

The fitness of the human population is degenerating 1-2% per generation.  Mutations are the result of physical entropy being manifested at the molecular level.  Like all machines, the bio-machinery affecting DNA replication, DNA repair, and selective elimination, all operate at less than 100% efficiency.  This degeneration is the opposite of Darwinian evolution.

There’s much more to the book than this, but this is enough for now. :)

Susan

Re: Junk DNA

Hey Susan,

I'm sick again, ugh. But no matter: it gives me more time to email, though less energy for thinking. 

Jon has turned out to be a fount of ideas to tick off to you. I imagine that a discussion between the two of you would cover much more ground more quickly. On the other hand, Jon's tendency towards beligerence, and our more developed relationship suggests to me that you and I have a better chance of convincing each other than you and him. 

Anyways, he makes the interesting point that there is more evidence that evolution took place than there is that the earth orbits the sun. There is no direct proof of either; there is only indirect evidence that supports these ideas, and testable hypotheses that come from these theories. But I belive that even you believe in the helio-centic theory based on all the indirect evidence that exists (you do, don't you?).  

As for the genetic entropy book, I've all but given up on it. I got about 70 pages into it and I've learned nothing, been convinced of nothing, and find his arguments contradictory, rambling, and frustrating. I try to keep an open yet sceptical mind with all that I read. For instance, I am not convinced by every argument that Dawkins makes in his books, though I am enthralled by most. Your creationist author did not even have convincing halves of arguments. Yes, he had lots of footnotes, but there's no reason to look at his sources since he never eeks out a coherent argument about anything. Most of the time I was left wondering, what is his point?  

Not only that, he's boring! There's nothing interesting in the book. I don't know how you can read it! And his news flashes make me want to punch him in the face (I tried to keep an open mind about them, but they got more annoying as time went on). 

If you want to bring up something that he touched on, feel free, but I got nothing from the book and so am left with nothing to talk about. 

The main problem with the book is that it sets out to punch holes in evolutionary theory by building up this really squirrelly idea that the human genome is deteriorating. Well, he does a terrible job of showing that the human genome is deteriorating, and he does a worse job of showing this would imply that evolution doesn't work. 

And what's with his crazy princess and the pea analogy? He totally goes through this whole thing about how natural selection can't ever possibly happen because of interactions at the genetic level, and then he goes on to say it does happen in the intra-species case.

Also, his math comes across very bad in a couple spots. 

Blech. 

Dawkins makes the point that if evolution is false, then there should be pretty easy tests that could be performed to disprove it. Go and find a fossil in the wrong layer. Find a clock that gives a different age of the earth. Find an animal with a shocking set of DNA. Don't go through some agonized description of one leaky idea like the genetic entropy book does.

Meanwhile, you have this other theory that says the earth is 10,000 years old. I have given you many, very simply understood tests for how to disprove that (e.g. The distance of stars). And the tests disprove it. You have to concoct some very crazy ideas to get around any of the tests. 

Why are you so resistant to tests? Come up with a couple. We'll carry them out.

-Brandon

PS I don't find junk DNA to be of crucial importance. I think you are latching onto the idea because it is a place where you see there might not be a scientific concensus. Just because scientists might be arguing about one detail of a theory doesn't mean the whole theory is wrong.  

Junk DNA

Hey Brandon,

Dawkins talked about ‘junk’ DNA and saw it as evidence of evolution and as a source of genetic material that could be rearranged through mutations in order to move to increased complexity.  As you read Sanford’s Genetic Entropy, you’ll see that he presents evidence against the idea of ‘junk’ DNA, saying that scientists continue to find that what had been thought to be junk is in reality very important and even crucial.  Here are a couple articles that align with Sanford’s assertions:

http://www.nature.com/news/2010/100331/full/464664a.html
http://www.princeton.edu/main/news/archive/S24/28/32C04/

Susan

Re: Neanderthals

Hey Susan,

Good job posting your first blog entry on your own. The formatting looks great; so you're clearly not having some of the issues I am (I've had to re-edit every entry I've made so far via email:).

As for Neanderthals, the new info coming out about them doesn't seek to prove evolution is true. It's just interesting science related to evolution and genetics. I agree with you, btw, that Neanderthals must have been, by definition, the same species as the larger group of our ancestors if they could breed with them. Could a resurrected Neanderthal breed with modern humans? Now that is a question I would be interested in having the answer to. (I know your answer already though;). 

-Brandon

re: Neanderthals

Hey Brandon,

Good article, although I don’t see that it necessarily supports evolution.  If ‘modern’ and Neanderthal people interbred, it would logically follow that Neanderthals were fully human.  Having certain traits, such as larger skulls and thicker bones, doesn’t necessarily imply that the Neanderthals were less human or were earlier examples of human evolution.  There are strains of people today who have traits that are markedly different from the average human population—for example, dwarves and Australian aborigines.  The traits that make these groups of people different don’t mean that these people are somehow less human or less evolved, although there have been times when people thought so, especially in the case of the aborigines, who at one time were often killed by Australian settlers who considered them to be less-than-human pests needing to be eliminated.  This is one example of how the theory of Darwinian evolution contributed to racism.

Susan

Neanderthals

Did you hear the news about the Neanderthals? The internets are blowing up with the news:

http://news.discovery.com/human/neanderthal-human-interbreed-dna.html

-b

"Weak coffee is fit only for lemmas." -Paul Turan

Book, etc.

Date: Sat, 1 May 2010 15:49:05 -0400
Subject: Re: Book, etc.
From: Susan
To: Brandon

Hey Brandon,

My first response to this email was a bit snippy—sorry.

For example, when water freezes, it goes from a more disordered liquid state to a less disordered solid one; however, at the same time, the heat energy lost by the water is gained by its surroundings, so total entropy does not change.  In the process of Darwinian evolution, each time a mutation occurs that makes DNA in an organism more ordered, there would have to be a corresponding increase in entropy in the organism's surroundings so that the total entropy still increases or remains the same.

Okay, so how does this help your position?  One thing I'm having trouble with here has to do with mutations.  Most observed mutations are harmful and would move the genome to greater disorder (greater entropy); even so called 'neutral' mutations move the genome to disorder to a slight degree, as they disrupt the normal pattern. This fits the SLT, which states that entropy in the universe always increases or remains the same.  Darwinian evolution requires 'good' mutations to bring increasing order/complexity, the exact opposite  of what normally occurs.  Because of this decreasing entropy occurring in the process of Darwinian evolution, there has to be some consistent mechanism occurring at each step of Darwinian evolution for the total entropy to stay balanced out according to the SLT.

How does an organism distinguish between 'good' mutations (that bring increased order/complexity) and 'bad' ones?  A corresponding increase in surrounding entropy has to accompany the 'good' ones (to result in equal or increasing total entropy according to SLT), but not the 'bad' ones, which naturally result in increased entropy.  What is the mechanism by which an organism's genetic entropy decreases (becomes more ordered) with a corresponding increase in entropy in the organism's surroundings?

Help me think through this.  Here's a very rough analogy based on the water example:

DNA (ice) + 'bad' mutation (heat) = more disordered DNA (water)

DNA (ice) + 'good' mutation (heat) = more ordered DNA (still ice? A bigger chunk of ice?)  + ??? (where does the heat go?)

In each equation, a mutation is being added to previously existing DNA.  In the first, the mutation results in greater disorder, while in the second, it results in greater order.

Susan