From: Susan
Date: Mon, Jul 11, 2011 at 3:00 PM
Subject: Re: 2nd law again
To: Brandon
2nd law again Hey Brandon,
Attached is an article about the 2nd Law of Thermodynamics and evolutionary theory. There’s also a back story to this—it was peer reviewed and accepted by a math journal, but the complaint of one blogger caused its acceptance to be rescinded. The author complained and received an apology and compensation for legal expenses.
Susan
Re: Are Dog Breeds Actually Different Species?: Scientific American Hey Brandon,
Have you ever been around when a batch of 17 year cicadas were hatching out? It’s happening here, now, and they’re an extremely noisy bunch of insects—they’re fairly quiet early in the morning, then as the day warms up, they become more active, making a loud, undulating whine in the trees, sometimes seeming very close, sometimes further away, and often both near and far. Sometimes, when I’m walking outside, their sound feels like a constant almost mind numbing roar; this has been going on for at least a week. And while the cicadas are making their noise, the crickets chime in periodically, and of course, birds are singing everywhere—it’s a regular cacophony of sound. Every so often the tree frogs add their voices, too. (I wish I could identify more birds by their songs—I do much better by sight.)
So you claim that adaptation and change can happen "within a kind," but that one "kind" cannot change into another. The major problem with your argument is that you don't define "kind."
Actually, I don’t think that’s a problem at all. The classification of organisms is a bit arbitrary and subjective, and even Darwinian evolutionists can’t agree on how to classify some organisms, especially now that organisms can be studied to the level of DNA. And evolutionary scientists also don’t all agree on the definition of “species”. Somewhere I read that “species” was originally just another word (from Latin, I think) for “kind” and was simply a descriptive term, but the word eventually became an official scientific term related to taxonomy. This is an area in which scientists still have much to learn, so neither creationists nor evolutionists can be totally adamant about which organism fits within which category, whether the evolutionist’s “species” or the creationist’s “kind”. In general, I’d probably say that if animals can reproduce with each other, they’re of the same kind—for example wolf and dog, or different breeds of dogs. I don’t know about foxes and coyotes because I don’t know if they can interbreed with dogs. Cats and dogs definitely don’t interbreed, so are of different kinds.
The point we’re discussing, though, is whether one type (kind/species, whatever) can morph into another type, which then morphs into something else, starting from one-celled organisms and ending up with man. Darwinian evolutionists assert that this can happen. Biblical creationists assert that, while variation and adaptation within a kind occurs, one kind does not change to another kind—the canine ‘kind’ does not morph into the feline or bovine ‘kind’, nor does the ape ‘kind’ morph into the human ‘kind’. Of all the studies I’ve seen presented by evolutionists, none have shown how one kind can develop from another. Darwin’s finches always remained finches. None of the thousands of generations of fruit flies that have been studied have yielded anything but fruit flies (many of which were grossly mutated, but they were still fruit flies). Of the thousands of years of farm husbandry, farm animals have always produced after their kind—bovines produce bovines, swine produce swine, and so on. In the studies of viruses and bacteria, the virus remained a virus, and the bacteria remained bacteria.
From a biblical creationist perspective, all the basic kinds of organisms appeared during the creation week at the beginning of time (Genesis 1). Mankind was made last and separately from all the other creatures. While there is no specific list of all the ‘kinds’ of organisms, it does say that each organism is to reproduce after its own kind: “Let the earth bring forth grass, the herb that yields seed, and the fruit tree that yields fruit according to its kind...” (Genesis 1:11) Likewise, the birds, sea creatures, and land animals were each created according to its kind. Just as apples always produce apples (and not peaches or beans), bacteria, molds, mammals, and humans each reproduce according to its own kind.
As for dog coats, you give one explanation for where the three genes come from: that God put all three genes and their variants in wolves, and people selected for them. Another explanation is the evolutionary explanation: that wolves had a certain set of genes, and as they were being domesticated, some of the wolf offspring had mutations in those genes that gave them coats that humans found charming. Then humans selected for these. And each time a new, charming mutation occurred, humans selected for it.
You’re apparently assuming that wolves were the first of the canine ‘kind’--how do you know that? Yes, I’m saying that the three basic genes were present from the beginning, and then variation resulted over time, whether due to human intervention or environmental conditions or other factors. That article stated that most variation could be accounted for by the mixing and matching of these genes. Mutation probably accounts for a small portion of the variation. For example, I believe the Mexican Hairless breed is the result of a mutation, as is presence of skin folds in sharpeis. Of course, in both breeds, negative traits go with the mutations—both breeds have ‘weak’ skin very prone to infections and allergies. Even with these mutations, sharpeis and the Mexican Hairless are still dogs—mutation changed some traits, but did not change their basic canine genome, the genes that make them canine rather than feline or something else.
It is mutations of genes that give the variety we see!
On what do you base this statement? Are you saying that these three genes for hair coats are all the result of mutations over time, and that there was a time, before the appearance of these genes, when all canines looked the same? And if these three genes weren’t present in the earliest canines, what determined the appearance of their coats? You’re making this statement as if it were a fact when, in truth, there is no way you can be sure of this. It appears that you are observing something in the present (presence of three genes for canine hair coat) and then interpreting its meaning about the past (that those genes appeared through mutation over time) from an evolutionary perspective. The study in the article used empirical science to learn about these genes; it determined how these genes function now, and while it determined that these genes account for most of the variation in canine hair coat, it says nothing about where those genes originally came from.
Apparently you believe that all wolves and dogs are related. How bout foxes? Coyotes? Are all birds related? Are bats related to birds? How can you tell? What about all apes? Are the monkeys related to apes? How bout bushbabies? (cuz they're super cute) Are camels related to horses? How can you tell? How do you know cats are not related to dogs? You seem pretty confident.
What do you mean by “related”? Most of these animals are classed as mammals because of morphological similarities. And these mammals are classified into various sub-groups on the basis of morphology. They are “related” in the sense that they have similar characteristics. But similar morphology doesn’t mean these animals are “related” in the sense of having shared ancestors. Bats are mammals that fly—they’re probably their own ‘kind’. I would also say that camelids, equines, felines, and canines are each different ‘kinds’. I imagine there are multiple ‘kinds’ of birds just as there are multiple ‘kinds’ of mammals. You seem fairly confident that all organisms are related through heredity in some way—on what are you basing your confidence?
I wish I could understand your integral that you wrote up. It may be trivial, but I think it’s neat that you have the knowledge to be able to write it.
Glad to hear you’re trying to keep some balance in your life by setting boundaries on your work. :o)
Congratulations to VJ! Didn’t know the major he chose existed—will he use it in his current job?
Susan
Hey Brandon,
Thought I’d send a few thoughts about that article, on the off chance that you might actually welcome a little conversation... :)
Creationists argue that speciation has never been seen.
The taxonomy of organisms is somewhat subjective. Scientists don’t always agree on how organisms ought to be classified. What does he mean by saying creationists argue that speciation has never been seen? Creationists have no problem with variation within a kind, such as all the different sorts of canines. It appears that the author wants to use the word speciation (in regard to the wide variety of dog breeds) in a way that misleads people into thinking that creationists do not believe that variation and adaptation occur.
For that matter, how does the author define ‘evolution’? If he’s merely defining it as ‘genetic change’, as the genetics book you recommended to me does, that definition is so broad that it would cover almost anything, including such things as variations in eye color, hair coat, or beak size. Again, creationists are fine with the idea of adaptation and variation within a kind. What they have a problem with is the idea that one kind can morph into another over time— say from canine to feline or from amoeba to man.
Take the many variations of hair texture, length, and color found in canines. Scientists have found that they all come from variants of three genes.
Just by mixing and matching... these three different genes, we could account for most of the variation that we see in coats in domestic dogs http://news.bbc.co.uk/2/hi/science/nature/8224519.stm
In other words, the many variations were developed by mixing and matching genetic material that was already present in the dog genome—no new material evolved.
Sometimes it would be nice to talk about something else. I like the debate, but when that’s all we talk about it makes things feel too one-dimensional—there’s more to us than just this.
Susan
On 5/3/11 12:39 PM, "Brandon Meredith" <mathcadd@gmail.com> wrote:
> http://www.scientificamerican.com/article.cfm?id=an-immodest-proposal
>
>
> Sent from my iPhone
Genetics book Hey Brandon,
Okay, I’ve gotten the genetics textbook and have started reading it. You’re correct in saying the book won’t help much in our discussion on creation/evolution other than giving us a foundation for discussing genetics.
I was hoping the book would say something about d- and l-isomers, but I don’t think it does—at least I haven’t found it yet. It then occurred to me that I might be more likely to find this in an organic or biochemistry textbook. Since I still have some of my old textbooks, I looked in them and found it quite easily.
The book’s definition of evolution: “genetic change among members of a population.” p.663 According to this definition, any change would be considered evolution. This definition conflates adaptation (variation within a kind, which I have no problem with) and macroevolution (change from one kind to another, such as monkey to man, or even prokaryotes to eukaryotes). The textbook appears to do an excellent job of explaining adaptation within a framework of genetics. On the other hand, it seems to be a bit lacking in explaining the ‘monkey to man’ type of evolution within the framework of genetics. Of course, the study of macroevolution primarily involves forensic science, while this textbook focuses on genetics from an empirical perspective.
An excerpt from chapter 17, on mutations: “Mutation is a fact of life. Our DNA is continually assaulted by spontaneously arising and environmentally induced mutations. The fact that most are detrimental is evidenced by the number of mechanisms that cells possess to reduce the generation of errors in DNA and to repair those that do arise.” (p.500)
So living organisms possess multiple mechanisms to correct mutations. Yet the build up of mutations is supposed to be a driving force in Darwinian evolution. I’ve not yet discovered from the book how the forward movement of Darwinian evolution is supposed to have overcome the resistance to change evidenced by the corrective mechanisms.
My results (Table 4) confirm several generally accepted facts about human spontaneous mutation: 1) well over 90% of all mutations are single nucleotide substitutions [Giannelli et al., 1999; Nachman and Crowell, 2000], 2) CpG context increases substitution rate by ~1 order of magnitude [Sommer, 1995; Nachman and Crowell, 2000], and 3) deletions are ~3 times more common than insertions [Gu and Li, 1995] so that mutation shrinks human genome by ~1 nucleotide per generation [Petrov, 2001]. [italics are mine] ...
The results reported here imply, in agreement with previous estimates [Vogel and Rathenberg, 1975; Kondrashov, 1988], that the total number of new mutations per diploid human genome per generation is ~100 (1.8 x 10tothe -8 x 2 x 3.2 x 10 to the 9=115). [couldn’t figure out how to make it write the correct symbols]
Kondrashov, A. S. 2003. Direct estimate of human per nucleotide mutation rates at 20 loci causing Mendelian diseases. Human Mutation. 21 (1): 12-27.
What I find interesting in the above study is the statement that mutations shrink human genome over time. This flies in the face of the Darwinian idea that mutations increase genetic information and complexity. If Darwinian evolution actually occurred, it would have had to overcome the loss of genetic information caused by mutations. [This study also seems to disagree with the genetics textbook in saying that most mutations are substitutions, while the genetics book states that insertions and deletions are more frequent (p.477). Since most of the references for chapter 17 are older than this article, this article is probably based on newer information than what was available for the book.]
In chapter 19, on genomics: “The reduced DNA content, fewer functional genes, and the large number of pseudogenes suggest that, evolutionarily, the genome of M. Leprae has undergone massive decay through time, losing DNA and acquiring mutations that have inactivated many of its genes... Regardless of the mechanism for gene inactivation and loss, this genomic decay helps explain some of the bacterium’s unique properties. Genes for many metabolic enzymes and structural proteins have been lost, which may explain why the bacteria cannot be cultured on synthetic media containing traditional carbon sources; it may also account for the bacterium’s slow growth.” (p. 553)
Here, we’re talking about the degeneration over time of the genome of the leprosy bacterium. I would call this genetic entropy. The book says that this particular genome has deteriorated over time. This poses a number of questions: How did this bacteria evolve forward from non life or a simpler organism to become the leprosy bacterium? What made this forward movement (from less complex to more complex) stop and begin to move backward (degenerate)? If this genome has degenerated over time, why wouldn’t we expect any other genome to degenerate over time? The Kondrashov study certainly indicates that the human genome has been degenerating (which agrees with the book on genetic entropy). What scientists routinely observe is degeneration over time. Where is the observation of the monkey to man sort of Darwinian evolution?
This is enough to begin with. Since you’ve had more time to read the book than I have, perhaps you’ve already found answers to some of my questions. And I’m sure you have questions of your own. I’m looking forward to hearing what you have to say. :o)
On a lighter note, snow is coming our way again—we’ve had quite a bit of cold and windy weather this winter. Of course, I don’t mind as long as I’m inside with a cheery fire in the fireplace. We’ve been keeping the bird feeders full, and it has been fun seeing all the different kinds of birds that show up.
Susan
Re: Genetics Book Hey Brandon,
Sorry I came across in such a negative manner—I certainly didn’t intend to. I was in a hurry when I wrote my last email, so perhaps that’s why the tone was a little off.
I’m thinking that reading this genetics book will help us find some common ground, at least as far as terminology, which should be very helpful.
Though I don’t always appear enthusiastic, I do always enjoy learning. :) And I do want to make sure that what I’m learning is true.
In particular, you claim that there is no such thing as a neutral or nearly neutral mutation. Well, the chapter on gene mutations shows exactly the mechanism by which a mutation can occur with absolutely no effect on the phenotype of the organism.
Of course a mutation can appear to have no effect on the phenotype of the organism. Mutations can affect body processes which aren’t outwardly apparent. If the mutation concerns something that will only be activated under certain conditions, that mutation may just sit there with no apparent effects on phenotype—until those certain conditions occur. Remember, genotype and phenotype aren’t the same. Another thing, organisms have built in corrective mechanisms which are able to ‘fix’ many mutations before they have a chance to cause harm. Both the books I sent you—Signature in the Cell and Genetic Entropy—address this issue of neutral or near neutral mutations. (The second is a little more direct, while the first one talks more about ‘junk’ DNA, which is supposed to be a conglomeration of mutations which have collected over time.) I’m looking forward to seeing how they compare with the book you recommended. Our discussion will go much better if you study the books I sent you while I study the one you recommended to me.
Since I'm on a roll, there's something that's been bugging me for a while. It's your argument that runs along the lines of "if everyone jumped off a bridge, would you?" I point out that the overwhelming majority of scientists across the globe point agree that evolution is correct, and you say "well, they could all be wrong." Of course you could be right, and all those scientists could have been wrong for 150 years, but would you at least admit that a vast scientific consensus on a hotly debated topic probably means something? To say that a scientific consensus doesn't convey any information at all in nonsensical.
I’ll concede that if most scientists agree on something, it is more likely to be correct. HOWEVER, the fact that most scientists agree on something has nothing to do with whether or not that idea is correct, and scientific consensus is not a proof. I can think of lots of ideas about which earlier scientific consensus was later proven to be wrong—the usefulness of the appendix and thymus, the need to wash hands and instruments between patients, the usefulness of leeches/bleeding to treat various illnesses, the perceived causes and best treatments for various illnesses, and so on. Today, some people claim that there is a scientific consensus, even when there isn’t one. For example, there is no real consensus about ‘global warming’ (there may be more of a consensus that it isn’t happening than that it is). And there are probably more scientists with a creationist perspective than you might expect. It’s just that you might not hear about them because they don’t follow the scientific PC thinking. And another thing—if the majority of educational institutions are teaching evolution only, they are naturally going to produce people who think from an evolutionary perspective. Some will be brave enough to think outside the box, but most will just absorb and reflect back what they have been taught. And if they want to become research scientists, they know that they’ll be more likely to get funding if they couch their research in the framework of Darwinian evolution.
But! the statement "a theory is true implies most scientists agree it is true" is hopefully, for the most part, almost always true.
I think what you’re saying here is, “If a theory is true, then most scientists will agree that it is true.” Is that correct? If so, I would have to disagree. For example, there was a time when most scientists agreed that the appendix was a useless appendage—those scientists believed something to be true which was, in fact, false. In this case, the consensus opinion was in error. The theory that the appendix is useful was true, but most scientists disagreed with that theory and chose to stick with the consensus theory. Somewhere along the line, some scientists began to question the consensus opinion, did further research, and discovered the usefulness of the appendix. Your statement would be in error every time a consensus idea was shown to be wrong.
Yes, you believe that evolution is wrong, but stop acting surprised when you see scientists using evolution!
I’m never surprised when I see scientists explaining things from an evolutionary perspective—after all, that’s the way most of them have been taught. What I take issue with is the idea that one must interpret everything from an evolutionary perspective in order to do good science. Belief in Darwinian evolution isn’t necessary in order to do empirical science. One doesn’t need to know exactly how we got here in order to study how things currently function in the present. Creationists and Darwinian evolutionists use forensic science, which is a whole nother ball game. I also take issue with educational institutions and scientists treating the theory of Darwinian evolution as if it were a fact which must never be questioned and need never be explained—it seems to me that such an attitude would tend to discourage critical thinking.
I like long emails. :o) The more you write, the better idea I have of how you’re thinking. It also makes me feel more connected. Wish you didn’t have a cold and were closer to family—I like being around family for Christmas. It actually snowed here on Christmas day—five inches—not much compared to Boston, but more than we’ve had since moving here over a decade ago. I read online that this is the first time Georgia and S. Carolina have had snow on Christmas since the 1880’s.
Take care,
Susan
Re: Fossil Finger DNA Points to New Type of Human | Wired Science | Wired.com Hey Brandon,
It’s disconcerting that the article ( http://m.wired.com/wiredscience/2010/12/denisovans/ ) opens up talking about a finger bone, but displays a photo of a tooth.
> However, kinetic calculations predict that
> small fragments of DNA (100–500 bp) will survive for no
> more than 10 kyr in temperate regions and for a maximum
> of 100 kyr at colder latitudes owing to hydrolytic damage
> (Poinar et al. 1996; Smith et al. 2001). Even under ideal
> conditions, amplifiable DNA is not thought to survive for
> longer than 1 Myr.
> http://rspb.royalsocietypublishing.org/content/272/1558/3.full.pdf+html?sid=1c
> ad9280-7246-49eb-b212-6f6358028c5e
This article discusses the viability of DNA over long periods of time. It finds that DNA in dead organisms degenerates over time, so that what appears to be indicating DNA of a different species may in fact simply be the product of postmortem degeneration. It’s also interesting to see that identifiable fragments of DNA would not be expected to survive over 10,000 years in a temperate region (where this part of Siberia is located). These findings fit much better with the biblical creation scenario than with the 40,000 years mentioned in the wired.com article.
Much of the rest of the article is conjecture based on interpreting evidence from an evolutionary perspective. I wonder how these scientists are defining ‘species’, since they acknowledge that these early humans probably interbred with other human populations. It would make more sense to describe these people as a different strain or variety, like the Australian aborigines or Eskimos—assuming that the DNA differences found aren’t simply the result of postmortem degeneration over time.
Susan
