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