Tuesday, September 4, 2007

Marcsana shows his true colors

Even after being informed of how unethical and indefensible quote mining is, Marcsana continues to do it.

I promised to call you out every time you quote mine, Marcsana. I cannot believe that, despite the exposition of quote mining for what it is, you continue to do it. This is nothing short of a mind-bogglingly unethical act. If you wish to call something “disgusting,” then such actions will fit the bill quite nicely.

From his comments on my post on Answers in Genesis:
But, as David Raup (Curator of Geology, Field Museum of Natural History) stated in 1979: “... some of the classic cases of darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information ...”.( 'Conflicts between Darwin and paleontology', Field Museum of Natural History Bulletin, Vol.50 No.1, January 1979, p. 25.) The horse argument has lost some of its zip in modern day thinking.

You're quote mining, Marcsana. Blatantly so.

Here is the real quote:
Well, we are now about 120 years after Darwin and the knowledge of the fossil record has been greatly expanded. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is still surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than we had in Darwin's time. By this I mean that some of the classic cases of Darwinian change in the fossil record, such as the evolution of the horse in North America, have had to be discarded or modified as a result of more detailed information — what appeared to be a nice simple progression when relatively few data were available now appears to be much more complex and much less gradualistic. So Darwin’s problem has not been alleviated in the last 120 years and we still have a record which does show change but one that can hardly be looked upon as the most reasonable consequence of natural selection. Also the major extinctions such as those of the dinosaurs and trilobites are still very puzzling.
And here are some more real quotes from the real article.
Part of our conventional wisdom about evolution is that the fossil record of past life is an important cornerstone of evolutionary theory. In some ways, this is true -- but the situation is much more complicated. I will explore here a few of the complex interrelationships between fossils and darwinian theory. . . Darwin's theory of natural selection has always been closely linked to evidence form fossils, and probably most people assume that fossils provide a very important part of the general argument that is made in favor of darwinian interpretations of the history of life. Unfortunately, this is not strictly true. We must distinguish between the fact of evolution -- defined as change in organisms over time -- and the explanation of this change. Darwin's contribution, through his theory of natural selection, was to suggest how the evolutionary change took place. The evidence we find in the geologic record is not nearly as compatible with Darwinian natural selection as we would like it to be.
Page 22
Now let me take a step back from the problem and very generally discuss natural selection and what we know about it. I think it is safe to say that we know for sure that natural selection, as a process, does work. There is a mountain of experimental and observational evidence, much of it predating genetics, which shows that natural selection as a biological process works.
Page 25
So what was this article really about?

It was about whether natural selection alone can account for all the changes we see in the fossil record. Raup argued (as have many other evolutionists, Stephen J Gould being perhaps the most prominent) that it cannot. He hypothesizes several ways in which such changes can be explained. He spends some time on a hypothesis he is well-known for (he later wrote a book on it entitled Extinction- Bad Genes or Bad Luck?)- that evolutionary change is often driven by causes such as meteor impacts that natural selection does not influence.

He is clear that he does not think he has all of the answers.
The ideas I have discussed here are rather new and have not been completely tested. No matter how they come out, however, they are having a ventilating effect on thinking in evolution and the conventional dogma is being challenged. If the ideas turn out to be valid, it will mean that Darwin was correct in what he said but that he was explaining only a part of the total evolutionary picture. The part he missed was the simple element of chance!
Page 29
And what does Dr. Raup think of creationists? He has written several essays pointing out the follies of creationism, among them "The Geological and Paleontological Arguments of Creationism" in Scientists Confront Creationism (one of my old favorites, recently re-released as Scientists Confront Intelligent Design and Creationism) One quote sums up his feelings quite well-
As I will show here, the rocks and fossils say YES to evolution!
Page 147

A sticky situation for Marcsana

Marcsana’s latest response in A creationism vs. evolution discussion,. Part 2 is extremely lengthy and wordy. I feel no need to address most of it here, as it’s just beating a dead horse- most of it is rehashing of the same arguments that have already been presented over and over again- truly “no new information!”- irrelevant side excursions, and failure to address most of the points I’ve already made. I’ll sum up Marcsana’s points in my next post.

However, the last section is so egregious as to demand addressing. It is apparent, when looking over this discussion, that most of Marcsana’s material consists of canned quotes and paraphrases from AIG. When he attempts to deal with something outside of the limited realm of AIG’s predigested responses, it is often obvious that he really does not know what he is talking about. This quote shows a profound lack of understanding of the subject at hand, an ignorance that is truly so appalling as to cast extreme doubts on any of Marcsana’s opinions on anything having to deal with matters biological.

Once again, Marcsana's original is plain text, my responses are in bold.

Let’s look at this quote line-by-line.

Not so fast. Your iron-sulfur surface does not capture and store the energy.

We have already shown that iron sulfide membranes generated in conditions simulating those of the early Earth can hold a tension of 500 millivolts," says Russell. "(That's) quite enough to drive a primitive metabolist
Metal cells may have held the chemicals of life's origin captive

Nor can the conversion mechanism be so simply stated. First, look at my post on your thermal vents. Then remember BOTH posts on Thermodynamics.

None of those posts have anything to do with this system.

The iron-sulfur surface more or less deals with acetate. This is for all intents and purposes an adhesive.

I must ask, Marcsana- have you ever taken a college-level class in any of the life sciences or in organic chemistry? You are somehow confusing acetate (a salt or ester of acetic acid, a vital compound in many organic reactions) with something like polyvinyl acetate, which is an adhesive. This is not a mistake that anyone with any training or education whatsoever in basic biology would make. If you don’t understand something as fundamental as the bare-bones basics of biology, how can you possibly make educated statements on any matters biological? Please don’t try to explain this away as a simple typo or a meaningless slip-up. This is somewhat Zen-like, but if you don’t realize how grave an error you made, you don’t have the knowledge necessary to realize how grave an error you made.

Let’s take a simple lesson in biochemistry and look at acetates and why they are important.

In order for life to exist, metabolism (chemical processes that occur inside cells) must exist. These processes convert energy into energy forms usable by cells (catabolism) or into components of the cells such as proteins (anabolism.)

These conversions occur through what are called “metabolic pathways,” through which the chemicals are transformed by enzymes. These pathways may be linear, such as photosynthesis (converting sunlight, carbon dioxide and water into glucose and oxygen) or cyclical, such as the Krebs cycle.

Many of these metabolic pathways show extreme conservation across phyla. For example, the Krebs cycle (often known as the citric acid cycle) is found in all organisms that utilize oxygen for cellular respiration. Cellular respiration has nothing to do with breathing; it’s how a cell obtains and uses fuel and disposes of the resultant wastes.

Glycolysis is the process through which cells break down glucose into pyruvate, in the process also releasing ATP, the currency of cellular energy. . In the presence of oxygen, the pyruvate is then converted, via pyruvate decarboxylation, into acetyl CoA, which is used in several cellular processes, but primarily in the Krebs cycle, where it provides carbon that is oxidized to form energy. The Krebs cycle is a vital part of the metabolic pathway that transforms nutrients (protein, fat and carbohydrates) into energy, carbon dioxide and water.

So what does this all have to do with acetates? Well, as you might guess from its name, acetyl CoA has something to do with acetates. An acetyl group is formed from acetate. So acetate is a vital compound in the chemistry of life, with the pyruvate decarboxylation reaction just one example of its use. And, quite obviously, it has nothing to do with “adhesives!”

So what does this all have to do with thermal vents?

One of the foremost authorities on the possibility of life first forming in bubbles at thermal vents is Dr. Michael J Russell of NASA and the University of Glasgow. All of the papers which I cite can be found here .

Russell postulates that the precursor to acetyl CoA pathway formed when carbon dioxide and hydrogen reacted with metal sulfides (such as iron sulphate) at hydrothermal vents.
Geologists have suggested that life might have emerged at hydrothermal vents, chemists have shown that metal sulphides such as FeS and NiS can catalyse biochemical reactions in the absence of proteins, and biologists have suggested that the acetyl-coenzyme-A (CoA) pathway of CO2 fixation might be very ancient. New findings from the enzymes at the heart of the acetyl-CoA pathway, carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS), indicate that metals and metal sulphides go the biochemical work of CO2 fixation. Here we propose that biochemistry got started when the two volatiles that were thermodynamically furthest from equilibrium on the early Earth – namely, marine CO2 from volcanoes and hydrothermal H2 – met at a hydrothermal vent rich in metal sulphides. In this ‘hydro-
thermal reactor’ hypothesis, a primitive, inorganically catalysed analogue of the exergonic acetyl-CoApathway, using H2 as the initial electron donor and CO2 as the initial acceptor, was instrumental in the synthesis of organic precursors to fuel primordial biochemical reactions. We suggest that primordial biochemistry was housed in an acetate-producing hydrothermal reactor that retained reduced carbon compounds produced within its naturally forming inorganic confines.
“The rocky roots of the acetyl-CoA pathway”
This theory helps explain not only the origin of various metabolic pathwhays that use acetates, but of enzymatic metal clusters that are very similar to those still used by many organisms today.
The slow trickle of hydrogen and carbon dioxide through such chambers and across the iron sulfide catalyst promotes formation of acetate, according to Russell and Martin. Acetate is a key intermediate in virtually all biosynthetic pathways, and in modern cells, enters these reactions tethered to sulfur. In modern bacteria, the two enzymes that make acetate depend on a catalytic core of iron, nickel, and sulfur, arranged almost exactly as they are in the free mineral itself. “In other words,” Russell and Martin have written, these enzymatic metal clusters “are not inventions of the biological world, rather they are mimics of minerals that are indisputably older, and which themselves have catalytic activity in the absence of protein”
Jump-Starting a Cellular World

These vents provided gradients of both pH and temperature that were more favorable to the production of organic molecules than hotter “black smoker” type vents.

The seepages are caused by convection of ocean water through hot crust composed mainly of magnesium and iron silicates (5). Exothermic hydration of hot rock would have maintained the convecting waters at ~100°C and pH ~10 (3). Gradients within such a porous seepage mound, from hydrothermal fluid to ocean, would have been from pH ~10to ~6 and from ~100°C to <20°c.>
“The Importance of Being Alkaline.”

And, to get back to the acetate…this theory also helps explain the origins of two different types of lipid membranes in prokaryotes (bacteria and other life forms without a nucleus) and eukaryotes (all other living things.)
[T]he scientists say that the prokaryotic branches of bacteria and archaea split while still contained within the iron sulfide birthplace. The ancestors of today's bacteria made one kind of lipid membrane, while the ancestors of the archaea generated lipids in a completely different way.
"Both the fatty acid lipids for bacteria and the isoprenoid lipids for archaea start from acetyl-coenzyme A, a truly universal intermediate," says Martin. "The function of the fatty acid and isoprenoid lipids is the same, but the route to get there differs. As a modern example, think of wings in insects and birds; those wings arose completely independently."
Metal cells may have held the chemicals of life's origin captive

Furthermore, the half-lives of adenine, uracil, guanine or cytosine won’t allow for a simple capture.

What in the world are you talking about? Where and how did the nucleobases come into this? Are you somehow thinking that the iron-sulfur system was postulated to “capture” bases? Again, do you understand what you’ve been reading? What you have written is meaningless gibberish.

You haven’t provided anywhere near a sufficient enough response to satisfactorily explain requirements three and four

As I have previously explained rather thoroughly, these “requirements three and four” are obstructionist creationist fabrications, not science. I will deal with them even more thoroughly in my next post.

In short, you need a “machine” already in place that can convert geothermal energy. This, of course, would take time to evolve. But it can’t evolve if the raw geothermal energy is bombarding whatever is in those vents.

Once again, you totally fail to understand the theory- both of the Second Law of Thermodynamics and of thermal vents. Please read what I have written above, plus the various quotes from Dr. Michael Russell, and if you care to address them, please address the exact specifics of the theory that I am discussing and that he has researched.

Think of the skin cancer analogy.

Yes- let’s think about that skin cancer analogy. Thinking about it- questioning its logic, whether it makes sense, whether it is used approipriately or is logically flawed, is exactly the right thing to do!

Hmmm…. “If a person stands out in the sun too long, he or she won’t get more complex. He or she will get skin cancer. Why? Because we can’t harness raw solar power.”

This analogy is utterly meaningless on several points-
- We cannot generalize from humans to the universe. Our abilities to handle raw solar power have nothing to do with the rest of the universe’s ability to do so. A seedling, for example, easily transforms that solar energy into complexity. All over the world, plants provide proof of local increases in complexity.
- It’s wrong, even when applied to humans. We may not be photosynthetic, but we can and do harness raw solar energy! Sunlight –specifically ultraviolet rays- is needed to produce vitamin D in the skin. Sunlight stimulates melanocytes to produce melanin and increase tanning.
- Like it or not, cancer can be an increase in complexity. Thus, cancer cause by sunlight can be viewed as an overall increase in complexity.

So I thought about your analogy. And I found it wanting, illogical, and irrelevant.

DNA and RNA are almost unimaginably complex and this proposed model can’t explain the rise of information. It is far too simplistic.

This argument is called “”the argument from incredulity” or “the god of the gaps.” Just because you cannot explain something doesn’t mean it cannot be explained. Throughout history, various gods were claimed to be the cause of all sorts of things that people could not explain, such as plagues, volcanic eruptions, and mental illnesses. As our scientific knowledge has grown, we have replaced such outmoded beliefs with scientific ones.

Monday, September 3, 2007

More responding to Marcsana on post 1

Once again, Marcsana's original is in plain text, my responses are in bold.

Here is a much shorter posting about probability. Statisticians say that for something to be impossible, the probability has to be 10 to the 50th power.

No they don’t. That’s something that William Dembski made up. It doesn’t have backing in the scientific community at all, and you won’t find it in any statistics textbook.

When you wrote about probability, you wrote this:
“The same is true of forming molecules. Even if the chances of forming a particular molecule are very tiny in one trial, if there are billions upon billions of trials, the chances of that molecule being formed are very great.”

[snip long post about an article on talk.origins]

I am not going to address the long insertion about what’s written on the talk.origins website, as I neither wrote it nor claimed it, and it’s mostly irrelevant to this discussion. I will address this bit, condensed somewhat for understandability:

Probability doesn’t work that way. Probability says that for each attempt, the odds are for this. You can’t look at all the attempts as an aggregate whole. Each individual attempt has the same odds of assembling itself. The lottery example holds no water. This assumes there is a prize and since evolution is undirected, there is no “prize.”

This is simply false. I am not looking at “evolution,” I am looking at the probability of a molecule forming. As for “You can’t look at all the attempts as an aggregate whole. Each individual attempt has the same odds of assembling itself. “- I think you have an extreme misunderstanding here- I am not sure where you took statistics, but you may want to talk to your professor! Of course you can look at the number of attempts as crucial to the outcome. That is what probability is all about. The more attempts, the greater the chances that an event will occur. I do not need to assume a “prize” or have a “direction” to calculate probabilities. Either something happens or it doesn’t.

“Evolutionists often try to bluff their way out of this problem by using analogies to argue that improbable things happen every day, so why should the naturalistic origin of life be considered impossible. For example, they say the odds of winning the lottery are pretty remote, but someone wins it every week. [snip more examples of the same] So they argue from these analogies to try to dilute the force of this powerful argument for creation.

In all the analogies cited above, there has to be an outcome. Someone has to win the lottery. There will be an arrangement of cards. There will be a pile of sand. There will be people walking across the busy street. By contrast, in the processes by which life is supposed to have formed, there need not necessarily be an outcome. Indeed the probabilities argue against any outcome. That is the whole point of the argument.”

This explanation makes absolutely no sense whatsoever, either logically or statistically. In the case of the lottery, there are two probabilities- either you win or you do not (or, in the case of a specific number being drawn, either that number is drawn or it is not.) Not winning is an outcome. In the case of a specific molecule forming, either it does or it does not. Not forming is an outcome. In both cases, a binomial distribution can be calculated. You may remember this formula from basic stats:
where p= the probability of an event occurring in one trial and q= the probability of an event not event occurring in one trial. Q is every bit as important to this calculation as P is. And, quite obviously, the larger the number of trials, the greater the chances that the event happens.

As with most things, evolutionists require that things be much simpler than they really are. Even all this aside, the probabilities are so high for the first cell to form, that it just can’t happen. There isn’t enough time in the universe.

You have not shown that.

This model was shown in http://www.talkorigins.org/faqs/abioprob/abioprob.html#Search

Creationists do this with probability:
Simple chemicals---bacteria

Evolutionists say it’s not that simple:
Simple chemicals—polymers—replicating polymers—hypercycle—protobiont—bacteria

I find it quite interesting that you cite this article (both here and above) yet you do not appear to have read it. It deals, quite elegantly, with all of the arguments that you brought up. Yet you use the same arguments this article so clearly refutes, without addressing them. The sections “Coin tossing for beginners and macromolecular assembly “ and “Search spaces, or how many needles in the haystack?” are especially relevant.

You cannot just pick and choose the parts of an article that you like.
Why, if you are going to use this article as a reference, do you not specifically address its conclusions?

But you still don’t get around information theory arguments.

Which have nothing to do with probability calculations. That's just deflection.

And this still doesn’t explain the first protein very well.

Explain what, exactly, about the first protein?

Nor does it offer how any of this is possible within the constraints of what we know about biology.

Actually, theories of organic molecule formation fit perfectly well with what we know about biology, and this article specifically addresses some of these points. You fail to give any examples of why they do not, nor do you specifically discuss the points in the article.

And it doesn’t show how each of these made those small leaps since it requires increasingly more information and proteins.

Actually, that is exactly what the model shows, and what the article discusses. Perhaps you should study each of the steps involved and address them directly.

If you truly wish to discuss probabilities, I recommend that you return to the article you cited twice, and actually deal with the arguments it presents, rather than throwing up yet another army of straw men.

Sunday, September 2, 2007

Responding to Marcsana on post 1

The discussion is getting a bit long in the comments to post 1 of our discussion on evolution, so I'm posting the comment and my response here. Marcsana's original is plain text, my responses are in bold.

Before I write about what the thermal vents theory presented, I would like to point out that this theory is far from agreed upon within the evolutionary community. In fact, origins is still a hot topic among evolutionists and there are many different theories out there competing for the prize, so to speak. Furthermore, this particular variant of the thermal vent theory is only one of several. If this theory was so solid, then everyone would agree on it. They do not.

This comment shows ignorance of what the scientific method is all about. Creationists often pounce on scientists for disagreeing about a theory, when such disagreement is at the heart of true science. Origin-of-life theory is a hot topic right now in science; as mentioned, there are several competing theories.

This is not a drawback of science. It is how science operates. It evolves- it gets better and more accurate as more information is discovered and incorporated into theories. Theories that don’t work get thrown out. Lack of agreement on a theory in no way invalidates it- only scientific evidence against it can do so.

And next, regarding Yockey. Isn't there another possibility? Can there be a chance that I'm not either dishonest or misinformed? What could I possibly be referring to? Oh, right. The fact that he is one of several scientists who hold to the idea of an old Earth AND a Designer. A creationist is someone who holds to a literal 6-day creation. We do differentiate. You also have an amazing ability to twist what I say or disfigure and misrepresent the creationist position. To that, I say that you should read what I write more carefully or be more honest. You have done this several times and I will deal with each one as I write the posts on various topics. Did I say Yockey was a "non-biased source?" NO! There is no such thing when it comes to origins which I treated in great detail. Maybe you didn't read it thoroughly. Origins deals with the unobservable, unrepeatable past. As such, one must have a preexisting bias toward a particular theory. Evolutionists prefer long ages and Christians hold the idea of a Creator. The question is interpreting the evidence we have which is what our discussion is about. Before you accuse me of dishonesty or misinformation, you better make sure that you have correctly understood what I wrote. I will call it out every time. Dr. Yockey is no friend to creation science and yet he still recognized the validity of the probability argument. That is why I chose the quote. He is not alone. I will treat probability again in another post.

The point still stands. Yockey is a biased observer; his word cannot be taken as impartial. As to the differentiation you attempt to make between various types of non-scientific belief systems regarding the origin of life- they are summed up very well by a quote from Leonard Krishtalka, director of the Natural History Museum at the University of Kansas-“Intelligent design is creationism in a cheap tuxedo.” As to “A creationist is someone who holds to a literal 6-day creation”- really? What about old-earth creationists, day-age creationists, gap theory creationists…

Let's take a closer look at thermal vents.

I wish that we would. Unfortunately, you don’t.

First of all, the theory of thermal vents posted here is not enough in and of itself.

I never claimed that it was. It is one small part of one possible mechanism for the evolution of complex organic molecules.

The following quote is from article at http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030396&ct=1.
"This metabolism-first model is not an alternative to life based on RNA. “We can't work without an RNA world either,” says Martin. But it does propose that geology at hydrothermal vents provided the structure in which life emerged, and suggests that understanding prebiotic organic chemistry at these vents may provide the key to understanding the emergence of life from nonlife."

I am baffled by the purpose of this quote. No one- including myself- posits that thermal vents are the only mechanism. And, as this quote clearly states, “understanding prebiotic organic chemistry at these vents may provide the key to understanding the emergence of life from nonlife.”

You asked me if I think acetates can form on an iron-sulfur substrate. Probably. But this has little to do with adenine, uracil, guanine or cytosine.

“You ask me if silicon can be smelted into glass. Probably. But that has little to do with strawberry jam, Kool-Aid, strawberry shortcake or Neopolitan ice cream.” You’re avoiding the question. No one thinks that RNA formed from nothing. There is no such theory. And thermal vent theories are very specifically not about RNA.

There are, broadly, two different realms of theories for the formation of the first complex organic molecules- RNA-first (as the paper you quote is concerned with) and metabolism-first (the theory I was discussing in my post) They are totally different (although not incompatible!) theories.

I will back up for a second.

You aren’t backing up. You are introducing a completely different topic. This is not a discussion of RNA-first theories.

Many evolutionists favor the "warm little pond" origin-of-life theory or the thermal vent theories because they postulate that the oldest known organisms are hyperthermophiles that would have required temperatures between 80 and 110 degrees Celsius.

A major problem for any of these theories is that adequate concentrations of certain complex compounds necessary for life are not accounted for. There has to be a requisite level of stability so that synthesis is at higher levels than degradation. What you proposed is an attempt to cover for these lacking components. By saying that those chambers function like cell walls is overly simplistic to say the least. While the vents you speak of may themselves be more stable (the one article mentioned they'd be stable for thousands of years...this is highly argumentative to say the least), we haven't yet touched the biggest problems with this proposed model. They have also been highly criticized because experimental research has shown that the half-lives of many vitally important compounds to be “too short to allow for the adequate accumulation of these compounds” (Levy and Miller, 1998, p. 7933)."

Once again- RNA-first and metabolism-first scenarios are totally different. Levy and Miller’s research has nothing whatsoever to do with metabolism-first theories. If anything, it actually supports such theories!

Levy and Miller go on to say that, "“unless the origin of life took place extremely rapidly (in less than 100 years), we conclude that a high temperature origin of life... cannot involve adenine, uracil, guanine or cytosine” because these compounds break down far too fast in a warm environment. In a hydrothermal environment, most of these compounds could neither form in the first place, nor exist for a significant amount of time (Levy and Miller, p. 7933)." They continue, "the rapid rates of hydrolysis of the nucleotide bases A,U,G and T at temperatures much above 0° Celsius would present a major problem in the accumulation of these presumed essential components on the early earth” (p. 7933). Below is the website:

You are showing a grave misunderstanding of the theory I am discussing. I don’t think you actually read the article you quoted from above, other than to pull an out-of-context unexplained quote from it. Once again- this theory is not about the evolution of RNA. It’s about the evolution of metabolic cycles before RNA. The article you discuss is totally irrelevant to this theory.

Can you please stick to the topic at hand and respond specifically to this article?

As a result of this, they theorized that either a two-letter code or an alternative base pair was used instead. This has the distinction of demanding an absolutely different kind of life was formed. This is not only highly speculative, but likely impossible because only A, U, G and T have the requisite properties for life. So now, life would have had to evolve completely differently than we know it today, and then re-evolve into the known code of life we see today. This change, by the way, appears to be impossible based on current knowledge of molecular biology.
And lastly, the authors found that given the minimum amount of time needed for evolution, cytosine is unstable even at temperatures as cold as 0 degrees Celsius. If Cytosine is lacking, then it is impossible to have DNA. It is also impossible to have RNA.

Again, the main thing that your argument does is strengthen the case for metabolism-first theories such as the one I discussed. You also have some misunderstandings and misrepresentations of the research. For example, the authors gave several possible theories of how nucleobases could have developed; some of which are possible at higher temperatures. The main point of this article is to present a theory that the nucleobases probably developed in frozen oceans rather than in a greenhouse atmosphere.

In addition, in the almost ten years since this paper was published, many theories have arisen that could allow development of nucleic acids in a prebiotic world- the PNA (favored by Levy and Miller) GNA and TNA , -first hypotheses and the PAH-first hypothesis . These theories can also explain the origin of self-replicating molecules at higher temperatures.

For a related source, see below:

Interesting. I had never heard of the author, “Jerry Bergman, PhD” or of his college, “Northwest State College.” A little research showed that Bergman probably shouldn’t be using the term “PhD”- In 1992 Bergman received his Ph.D. in human biology from Columbia Pacific University, a now defunct nonaccredited distance learning school. Columbia Pacific University lost its state approval to operate in 1995 and was ordered to close permanently in October 2000 by the State of California.
In another incident, he lied to the staff at Bowling Green State University, claiming he had a PhD when he did not. When he was fired for this and other ethical improprieties, he responded with a flurry of lawsuits complaining of “religious discrimination”- all of which he lost, in four different venues.

Of course, we cannot base our evaluation of the material in this article on his personal shortcomings- facts can be judged only on their own merits. As for the article - it’s typical creationist claptrap, composed almost entirely of quote mining, with no original research whatsoever. All of the points made in this article have been refuted many times, (check the Index to Creationist Claims as a start)

In conclusion, the thermal vents theory speculated on is nowhere near as strong as presented and it is clearly seen why not everyone in the evolutionary community is ready to jump on board.

You never discussed the thermal vent theory. The entirety of your comment on it was the word “Probably.” You discussed a totally different theory.

We also have the problems of the Second Law of Thermodynamics and probability. These will be treated again in other posts.

‘If there were a basic principle of matter which somehow drove organic systems toward life, its existence should easily be demonstrable in the laboratory. One could, for instance, take a swimming bath to represent the primordial soup. Fill it with any chemicals of a non-biological nature you please. Pump any gases over it, or through it, you please, and shine any kind of radiation on it that takes your fancy. Let the experiment proceed for a year and see how many of those 2,000 enzymes [proteins produced by living cells] have appeared in the bath. I will give the answer, and so save the time and trouble and expense of actually doing the experiment. You would find nothing at all, except possibly for a tarry sludge composed of amino acids and other simple organic chemicals. How can I be so confident of this statement? Well, if it were otherwise, the experiment would long since have been done and would be well-known and famous throughout the world. The cost of it would be trivial compared to the cost of landing a man on the Moon… . In short there is not a shred of objective evidence to support the hypothesis that life began in an organic soup here on the Earth.’

Sir Fred Hoyle, British physicist and astronomer, The Intelligent Universe, Michael Joseph, London, 1983, pp. 20-21, 23.

I should add that Sir Fred Hoyle was a proponent of 'intelligent cosmic control.' This quote is very much in line with the context.

Again, this quote has absolutely nothing to do with the theory that I am discussing.

I also hope you do realize that science is not a quote contest. A quote by itself is meaningless and proves nothing. Instead, one must look at several factors- who said the quote, is that person an authority on the subject, are that person’s views being represented fairly and completely, and (perhaps most importantly) how does the scientific community as a whole regard that person’s words and work?

Hoyle’s quote fails here on several counts. He was not a biologist or chemist; he was an astronomer. His pronouncements on biochemical theories are thus no more authoritative than a chemist’s speculations on whether Pluto is a planet.

As for his authority- he was well-known for clinging to theories that had no real backing. Creationists often claim that scientists cling tenaciously to outdated and disproven theories even in the face of massive evidence against them. While this is not true of scientists as a whole, it was true of Hoyle.
In the end, mounting observational evidence convinced most cosmologists that the steady state model was incorrect and that the Big Bang was the theory that agreed best with observations, although Hoyle clung to his theory, mostly through criticizing the interpretation of astronomers' observations. In 1993, in an attempt to explain some of the evidence against the steady state theory, he presented a modified version called "quasi-steady state cosmology" (QSS), but the theory is not widely accepted.

The evidence that resulted in the Big Bang's victory over the steady state model, at least in the minds of most cosmologists, included the discovery of the cosmic microwave background radiation in the 1960s, the distribution of "young galaxies" and quasars throughout the Universe in the 1980s, a more consistent age estimate of the universe and most recently the observations of the COBE satellite in the 1990s, which showed that unevenness in the microwave background in the early universe which corresponds to currently observed distributions of galaxies.
While creationists delight in quoting Hoyle’s words on abiogenesis, they neglect to tell the full story behind his remarks- he was an atheist and believed that life on Earth originated from material such as bacteria, viruses and insects spread by comets and interstellar debris, perhaps intentionally by intelligent extraterrestrial beings. As for his specific arguments against abiogenesis, they have been refuted so often that they are known as “Hoyle’s fallacy.”

Monday, August 27, 2007

The answers about Answers in Genesis-part 2

To the quote mines we go- part 1

Is Answers in Genesis, probably the site most highly-regarded by young-earth creationists and much used as a source by Marcsana, a reliable and reputable source that is above quote mining?

Um- no.

To start with, AiG touts the book That Their Words May Be Used Against Them – Quotes from Evolutionists Useful for Creationists, a 500-page book of nothing but hundreds of quotes, without context or information. It’s clear from the title of the book what its purpose is- and that purpose is most definitely not careful, thoughtful scholarship. Indeed, of the four quotes from scientists that I discussed in my first installment on quote mining, all four appear in this book! Undoubtedly, many of the creationist quote mines in existence are drawn totally from this compendium. No scholastically-responsible organization would promote such a book; this is even lower than a Cliffs Notes of creationism in scholarship.

This book-shilling takes place on AiG's own quote mine page. To explore all of the problems here would take a book- not only are the usual out-of context quotes offered here, there are quotes over a century old, quotes from sources that have nothing to do with evolution at all,
vicious personal attacks
Both of these statements [on atheism]1,2 were made by an arch-enemy of creationists, scientist and science fiction writer Isaac Asimov. His irrational atheism, the reason for his opposition to creationism, showed quite plainly in these two statements that the argument over creation/evolution is not about facts. When it comes to science, Asimov claimed to be interested in reducing the lack of knowledge, but when it comes to God, Asimov preferred to remain ignorant. And let’s not forget that this is exactly what Asimov was—deliberately ignorant. He was always interested only in the facts which suit him, not in all the facts, as is plainly shown in these two quotes.

and even quotes from mass murderers .

The first link on this page, after the book sale, is “99 Quotable Quotes.” A quote mine within a quote mine! The vast majority of these quotes have absolutely nothing to do with science and are not from scientific sources, unless one considers the Satanic Bible or News of the Weird works of science. I will take a look in my next posting at some of the ones that sound even marginally scientific.

In addition. AiG also has a series of webpages, variously called “Quotable Quotes” and “Quotes to Note,” featuring the latest quotes they have mined, again, with no context or explanations. In many cases, the true origin of these quotes is impossible to track down- many are said to be from lectures, often given in another language.

Many of the quotes that AiG cites are remarkable in their lack of context. Without any explanation or background, these quotes are so innocuous- or so true- as to puzzle non-creationists as to their reasons for inclusion- are they objectionable simply because they mention evolution or the political machinations of creationists? These are a few such quotes, presented in their entirety as they are on AiG's webpages.:

From “99 Quotable Quotes.”
43 “Human beings are made up mostly of water, in roughly the same percentage as water is to the surface of the earth. Our tissues and membranes, our brains and hearts, our sweat and tears—all reflect the same recipe for life, in which efficient use is made of those ingredients available on the surface of the earth…”
“But above all we are oxygen (61 percent) and hydrogen (10 percent), fused together in the unique molecular combination known as water, which makes up 71 percent of the human body.
So when environmentalists assert that we are, after all, part of the earth, it is no mere rhetorical flourish. Our blood even contains roughly the same percentage of salt as the ocean, where the first life forms evolved. They eventually brought onto the land a self-contained store of the sea water to which we are still connected chemically and biologically. Little wonder, then, that water carries such great spiritual significance in most religions, from the water of Christian baptism to Hinduism’s sacred water of life.”

Al Gore, “Earth in the Balance”, pp. 99-100
45 “Human evolution, of course, is responsible for our very long period of childhood, during much of which we are almost completely dependent on our parents. As Ashley Montagu first pointed out decades ago, evolution encouraged the development of larger and larger human brains, but our origins in the primate family placed a limit on the ability of the birth canal to accommodate babies with ever-larger heads. Nature’s solution was to encourage an extremely long period of dependence on the nurturing parent during infancy and childhood, allowing both mind and body to continue developing in an almost gestational way long after birth.”

Al Gore, “Earth in the Balance”, p. 229
59 “As for the claim that evolution is an unproved theory, that’s nonsense, Evolution is a fact, established with the same degree of confidence as our ‘theory’ of disease, and the atomic ‘theory’ of matter. Yes, there is lively debate about the particular evolutionary mechanisms that caused particular changes, but the existence of evolutionary change is not in doubt. Our own bodies provide walking evidence.”

Jared Diamond, “Who Are the Jews?”, Natural History Vol. 102, No. 11, November 1993, p. 19
60“Actually, there is superabundant evidence for animals evolving under our eyes: British moths becoming darker since the Industrial Revolution (industrial melanization), insects evolving DDT resistance since World War II, malaria parasites evolving chloroquine resistance in the last two decades, and new strains of flu virus evolving every few years to infect us.”

Jared Diamond, “Who Are the Jews?”, Natural History Vol. 102, No. 11, November 1993. p. 19,

From Quotable Quotes:
The problem won’t go away—we face a highly organized, well financed effort to legislate creationism—religious doctrine—into public education. … individuals opposing this effort to introduce theology masquerading as science into biology classrooms desperately need the help and support of professional biologists

Wayne A. Moyer
Executive Director
National Association of Biology Teachers (U.S.A.)
in Bio Science March 1980
Taken completely out of context, as AiG did, these quotes, if anything, support the theory of evolution. Of course, in many cases, AiG has convoluted arguments elsewhere on their site that attempt to refute the premises behind some of these quotes. But, standing alone without background, explanation, or reason, these quotes in and of themselves seem like statements of reason, not the ranting of the disillusioned.

Friday, August 24, 2007

Changes and memories

Last weekend, as part of my research on creationist quote mining, I visited parts of the UCSD campus I haven't seen in years. I planned a trip first to the Undergraduate Library on Revelle campus (they should have Science and Smithsonian) and then a jaunt to the Science and Engineering Library in Urey Hall. While I've paid several visits over the years to old haunts on Muir campus, it has been many years since I've been to Revelle.

I parked behind the Revelle dorms near the Undergraduate Library building, on a summer day where even the La Jolla coast was 95 degrees. Not a day for hiking. I headed up the ramp to UgLi...which was now some sort of computer lab. No books in sight. I guess the undergrads at UCSD don't need their own library any more...

Ah well, on to Urey. I knew they had remodeled the building a while back when earthquake-retrofitting it. There were new buildings behind and in front of it, all that stood out as glaring inaccuracies in my old visions (that shouldn't be there!) On my way, I passed the Revelle Commuter Lounge- a place that holds more memories for me that any other save the stairwells of Muir Campus. The endless impromptu bridge games, political punditries on the blackboard, birthday parties, first meetings... I was relieved to see it still existed- larger now, the couches looked comfier, and the walls were covered with murals.

So I got to Urey, walked in the glass doors (same whoosh, same distant elevator sounds, same smells of old paper and cement) and found that where the library once stood were now offices for the Bio department. I knew the library still existed... I had looked up the hours to make sure it was open on a Sunday. But where did it go? I poked around, wilting in the heat, and finally spied a grad student with a red Mohawk, who gestured in the distance and stated "They moved it to Geisel."

Geisel? Perhaps that was one of the new buildings? No, wait...I had seen a story in the paper a while back- that was the new name for Central Library, the architectural symbol for the whole campus. Of course, Central was also a fair walk from Revelle! So off into the heat...and into more disruptions of my mental maps! Gone were the wood-paneled buildings of the Student Center between Muir and Revelle; they were in the process of being replaced by a gigantic glass edifice from which wafted smells of curry and cinnamon buns. Mandeville was refreshingly unchanged; even the art galleries looked the same. As I descended into the Rectilinear Forest behind Mandeville, I could see that the Ugly Bird remained on his perch, but the bare stone arch was now completely covered with ivy.

Very little of the Rectilinear Forest remained. The then-new Staff Center was encroaching on one edge when I left UCSD, now a scramble of buildings had invaded from the Warren side as well. If anything, the remaining eucalyptus trees seemed scrawnier than I remembered. The Purple Volleyball Net still meandered through the forest- but now it was blue. The Talking Trees still murmured; one seemed to be giving a recitation of bird calls from a field guide.

I finally made it to Central- oops, Geisel- and into air-conditioned bliss. The card catalogs had changed; the black and green terminals of Melvyl had matured into the full-color Internet-enabled Roger- but the hunt remained the same. The atavistic joy of lifting down a musty old volume of bound journals, turning the yellowed pages until I found what I sought- that, at least has not changed in the past 20 years, no matter how the surroundings have changed in the interim.

Thursday, August 23, 2007

The answers about Answers in Genesis-part 1

Anyway, if you want a good angle, stop treating this as a matter of a religious organization making a brave effort against the forces of godless science. It's not. It's an exceptionally lucrative business organization profiting off the ignorance of large numbers of people making a major push to increase their influence and income.
Answers in Genesis (AiG) is perhaps the best-known of the creationist organizations in the US. It maintains a huge and attractively-designed website, sells an entire library of creationist materials, and runs the "Creation Museum" in Petersburg, KY. AiG is registered with the IRS as a 501c3 tax-exempt charity and pulled in over 13 million dollars in revenue in fiscal year 2005-2006. Of that 13 million, almost six million was paid out in salaries to board members and employees.

Charity Navigator, one of the most well-respected evaluators of charities, gives AiG 2 out of 4 possible stars, a rating that equals "Needs Improvement." For 2006, AiG performed worse than over 70% of other charities in how much it spent on programs and services, and its program expense growth was greater than its primary revenue growth, resulting in a net negative working capital ratio. AIG's rating has dropped steadily for the last 3 years, even as it has taken in more and more money.

Ministry Watch, which reviews only Christian ministries, although it names AiG one of its favorite ministries on the strngth of its evangelical fervor, rates AiG 405th of 430 organizations in financial efficiency.

So where is the money coming from, and where is it going? As a 501c3, AIG files Form 990 with the IRS every year. I looked at the data from 2002-2006.

Several interesting points can be made. AiG's chief staff are making an extremely comfortable living from their "ministry." Here are the highest-paid staffers and board members for 2006:

Ken Ham-President/CEO $124,615
Dale Mason- Vice President $114,301
John Pence-Director of planned giving/legal counsel- $96, 577
Mike Zovath-Vice President $88,269
James Hatton- Controller $88,269
Mark Looy-VP of Ministry Relations- $88,269
Kathy Ellis- Director of Administration- $82,038
Carl Kerby-Board Member $80,580
Patrick Marsh- Director $75,288
Dan Zordel- Director of Product Development $67,916
Mike Riddle- Speaker $67,769
Paul Varnum-Director of Video Productions $67,570
Tom Miller- Director- Events Outreach $66,269
Rod Martin- Director of Internet Services $64,848

In contrast, of the 22 religious charities in the same expense bracket as AiG that were rated as four-star charities by Charity Navigator and had Form 990s on file, none had the number of highly-paid board members and employees that AiG does. While AiG has 28 employees or board members with salaries of over $50,000 a year, only one organization, World Harvest Mission, had as many people with salaries over $50,000- but they were all employees; all of its board members served at no cost. Across all of the 22 organizations, the average number of board members paid over $50.000 was 2 and the average number of employees paid over $50,000 was 4. Ten of the organizations had no employees who received compensation over $50,000 and six had no board members who received any compensation at all. In contrast, AiG had 9 board members and 19 employees who received salaries of $50,000 or more in 2006.

In the following table, "Year" is the year of the Form 990 on file, "BM" is the salary of the highest-paid board member, "Employee" is the salary of the highest-paid employee, "Emp. 50K" is the number of employees paid over $50,000 yearly, and "BM 50K" is the number of board members paid over $50,000 yearly.

Examination of Form 990s reveal some other interesting patterns as well. For example, in 2003, former CEO Bill Wise bought a 2002 Toyota Camry from AiG. Although the car was valued at $15,089, Wise payed only $7.00- yes, seven dollars- for it. That same year, Wise received a computer worth $1105 for zero dollars. It is interesting that 2003 was Wise's last year on the board...

In future installments, I will look at some even more unsavory practices of AiG, such as their numerous ventures into quote mining and their legal woes.

Sunday, August 19, 2007

The quote mine collapses

In our discussion of evolution, Marcsana has made generous use of quotations, mostly unreferenced. However, in discussion of the second post in the series, he presented a list of quotes titled "Scientific Authorities speak on the 2nd Law [of Thermodynamics]." When called to task on the veracity of these quotes, his response was simply "Ignore the quotes at the end then if you want to."

No, I will not ignore them. They are prime examples of creationist quote mining, and they absolutely mandate a response. The use of such quotes is not fair debate; it is unethical and indefensibly shoddy scholarship.

Quote mining is defined as
...the use of a (usually short) passage, taken from the work of an authority in some field, which superficially appears to support one's position, but [from which] significant context is omitted and contrary evidence is conveniently ignored.
- The Quote Mine Project
Quote mining is so common in creationist propaganda as to be ubiquitous. There are dozens of sites that contain little content other than such disjointed, out-of-context quotes.

Obviously, such quote mining is not ethical, reputable or tolerable scholarship. Why, then, do creationists do it?

There are three possible reasons that I see:
  • Deliberate misrepresentation
It is clear that the original users of these quotes deliberately and knowingly used them inappropriately. There can be no other conclusion when the quote is taken out of context, and all material contrary to the creationist's point is deleted.
  • Ignorance
Some creationists truly may be unaware that some of the material that they read is deceptive or untrue. They may believe that those who write creationist materials would never be deliberately deceptive or misleading. They may be so unaware of the scientific method or of the process of logical thought and debate that they believe that lists of quotes can, by themselves, somehow prove something.
  • Laziness
Undoubtedly, much of the creationist quote mining is due to simple mental sloth. Fact-checking quotes and making sure that they actually are a true representation of an author's viewpoint can be hard work. Documenting the five quotes I discuss below took a couple of hours of Internet research and trips to two university libraries, plus time to actually read the original source materials. However, even a cursory search for the originals would have turned up enough information to document that the quotes were most likely not being used in an appropriate, context-sensitive way. For example, anyone who had even a vague understanding of the work of Ilya Prigogine would know enough to realize the usage of the quote discussed below was not accurate, and a very short search would have documented that the quote was taken from a paper on how evolution under the Second Law of Thermodynamics is possible. This would be enough to cast doubt on the usage of such a quote.

The following is a discussion of each of the quotes Marcsana used. The "References on creationist websites" is how many hits I got on Google for the complete quotation. In many cases, other websites exist that use different versions of the quotation. In the "Actual Quote" section, text missing from Marcsana's quotes appears in blue. "Selective quotation" refers to whether only those portions favorable to a creationist viewpoint were quoted, thus distorting the quote.

Marcsana's quote: There is thus no justification for the view, often glibly repeated, that the Second Law of Thermodynamics is only statistically true, in the sense that microscopic violations repeatedly occur, but never violations of any serious magnitude. On the contrary, no evidence has ever been presented that the Second Law breaks down under any circumstances.
Purported to be from: A.B. Pippard, Elements of Chemical Thermodynamics for Advanced Students of Physics (1966), p. 100.
References on creationist websites:
3, example Institute for Creation Research
Actually from: The source is correct.
Actual quote:
Although very few hypothetical experiments employing fluctuations have been analyzed in such detail, it appears most probable that they all fail to violate the second law on account of the necessary entropy generation by the observer who controls the process. There is thus no justification for the view, often glibly repeated, that the Second Law of Thermodynamics is only statistically true, in the sense that microscopic violations repeatedly occur, but never violations of any serious magnitude. On the contrary, no evidence has ever been presented that the Second Law breaks down under any circumstances, and even the entropy law appears to have an almost universal validity, except in such futile experiments as we have discussed above, the removal and reapplication of constraints.
Selective quotation:
Yes. This quote is discussing an entirely different concept than the common, unspecific definition of "entropy," and, as it applies only to closed systems, is even more irrelevant to discussions of evolution.
Out-0f date:
Yes. This is a quote from a textbook that is 50 years old- first published in 1957. Explanation: As is fairly obvious, this quote is from a physics textbook. The entire textbook is searchable online. The chapter it is in, titled "The Thermodynamic Inequalities," is specifically about the effects of entropy in closed systems, not open ones. In addition, this discussion is strictly about the strict physics definition of entropy as the unavailability of energy to do work. Nothing in this quote (or in this book) has any relevance to the probability of evolution. In fact, the word "evolution" appears nowhere in this book.

Marcsana's quote:No matter how carefully we examine the energetics of living systems we find no evidence of defeat of thermodynamic principles.
Purported to be from:
Harold Blum, Time’s Arrow and Evolution (1962), p. 119.
References on creationist websites: 8. Example: Scientific Evidence for Creation
Actually from: The source is correct.
Actual quote: No matter how carefully we examine the energetics of living systems we find no evidence of defeat of thermodynamic principles, , but we do encounter a degree of complexity not witnessed in the nonliving world. As compared to the in vitro photochemical and autoxidative reactions with which the chemist is more familiar, the complexity of autotrophic processes seems obvious, as is also the complexity of the step reactions in biological oxidations compared to the direct combustion of the same substances. To be sure, it is altogether probable that as investigation continues a relatively simple theme will be found connecting all the more or less isolated facts regarding energy metabolism in living systems, and indeed we have already evidence of that theme. But it seems certain that, simple or not in a general sense, quite complex molecules are involved. To be convinced of this one need only recall the role of enzymes in both the expenditure and accumulation of free energy. Most of the steps in biological oxidation require these substances, and their presence is also obligatory for CO2 reduction, whether by photosynthesis or chemosynthesis. The enzymes themselves are highly complex molecules, the specificity of their action being apparently associated with this complexity. But such molecules, and the reproduction of their complex patterns, is a subject to be taken up in the next chapter.
Selective quotation: Yes. This chapter was discussing some implications of the First Law of Thermodynamics (matter and energy cannot be created or destroyed) and how they related to energy production and storage in living systems. The chapter following this discusses how complex molecules are formed.
Out-0f date: Yes
. This book was first published in 1951 and is now 56 years old. Explanation: This book, while now significantly outdated, was perhaps the first to attempt to explain how evolution was possible under the Second Law (the "Time's Arrow" of the title.) It went into quite a bit of detail on how complex molecules could form, for example. Here are some of the author's discussions on the Second Law.:
(page 204) The second law of thermodynamics says that left to itself any isolated system will tend toward an increase in its entropy or randomness. Yet we see living sytems developing and maintaining what appears to be high complexity and organization, out of what seem relatively random surroundings. Does this mean that they do not obey the second law of thermodynamics, which we take for granted applies to all nonliving things? It has been pointed out repeatedly in the foregoing chapter that such a question only arises if we fail to grasp what is implied in the term "isolated system" when used in a thermodynamic sense, that is, a system which is isolated from exchange of energy with its surroundings. [He then goes on to give the example of sugar crystals forming in a cooling saturated solution, where the orderliness of the crystals is set off by the increase in entropy as heat is lost from the reaction.]
(pages 5 and 6) Within our short span of life we are continually aware of the irrevocable passage of time- aware that the same events never exactly repeat themselves whether we wish or no. Viewed in perspective, evolution is characterized by the same one-wayness in time, occasional statements as to its reversibility notwithstanding. It would be useful to us, as evolutionists, if there were some measure of this one-wayness of events. Science offers only one widely general principle which seems applicable; the second law of thermodynamics. One way of stating this law is to say that all real processes tend to go toward a condition of greater probability. Sir Arthur Eddington showed insight into the bearing of this law upon our problem when he described it as "time's arrow." This implies that the second law of thermodynamics points the direction of all real events in time, although giving no indication of the speed with which they happen. It should be tempting, then, to explore the relationship between time's arrow and organic evolution. Few, if any, physical scientists would hesitate to apply the second law of thermodynamics to the evolution of the nonliving world; yet even here its applicability may be worth examining. For the second law is in a sense an empirical and pragmatic law which owes its acceptance to the fact that it has worked whenever it has been put to test. The second law can be tested by setting up a self-inclusive system, deducing the changes that should occur, and accurately measuring these changes to see if they agree with prediction. In a sense, we may be accused of rigging the data to obtain agreement, but the fact that we have never failed to obtain it encourages our belief that we deal with a universal principle. Before any claim of a failure of the second law of thermodynamics with regard to any aspect of the nonliving world could be taken seriously, there would have to be absolute assurance that the system involved had been properly set up for examination. There have been numerous successful applications of the second law of thermodynamics to different aspects of living systems; these encourage the belief that this principle also applies there in a more general sense. Nevertheless, there are from time to time assertions that living organisms manage in some way to violate this principle. In such instances it does not appear that the system has been set up in such a way that it would be possible to reach the conclusion implied, but such statements are likely, because of their dramatic character, to have unwarranted influence on general thought.
In short, then, Blum explains yet again what has been detailed many, many times- evolution does not violate the Second Law.

Marcsana's quote: Another way of stating the second law then is: ‘The universe is constantly getting more disorderly!’ Viewed that way, we can see the second law all about us. We have to work hard to straighten a room, but left to itself it becomes a mess again very quickly and very easily. Even if we never enter it, it becomes dusty and musty. How difficult to maintain houses, and machinery, and our bodies in perfect working order: how easy to let them deteriorate. In fact, all we have to do is nothing, and everything deteriorates, collapses, breaks down, wears out, all by itself -- and that is what the second law is all about.
Purported to be from:
Smithsonian Institute Journal, June 1970, p. 6
References on creationist websites: 7. Example: ChristianAnswers
Actually from: Isaac Asimov, "In the Game of Energy and Thermodynamics, You Can't Break Even" Smithsonian, August, 1970
Actual quote:
Another way of stating the second law then is: ‘The universe is constantly getting more disorderly!’
Viewed that way, we can see the second law all about us. We have to work hard to straighten a room, but left to itself it becomes a mess again very quickly and very easily. Even if we never enter it, it becomes dusty and musty. How difficult to maintain houses, and machinery, and our bodies in perfect working order: how easy to let them deteriorate.
In fact, all we have to do is nothing, and everything deteriorates, collapses, breaks down, wears out, all by itself -- and that is what the second law is all about.
You can argue, of course, that the phenomenon of life may be an exception. Life on earth has steadily grown more complex, more versatile, more elaborate, more orderly, over the billions of years of the planet's existence. From no life at all, living molecules were developed, then living cells, then living conglomerates of cells, then worms, vertebrates, mammals, finally man. And in man is a three-pound brain which, as far as we know, is the most complex and orderly arrangement of matter in the Universe. How could the human brain develop out of the primeval slime? How could that vast increase in order (and therefore that vast decrease in entropy) have taken place? The answer is it could not have taken place without a tremendous source of energy constantly bathing the Earth, for it is on that energy that life subsists. Remove the Sun and the human brain would not have developed-or the primeval slime, either. And in the billions of years that it took for the human brain to develop, the increase in entropy that took place in the Sun was far greater- far, far greater- than the decrease represented by the evolution of the brain.
Authority of authors: Asimov is extremely well-known and wrote many books on science for the layman. He was a professor of biochemistry.
Selective quotation:
Yes- very much so! As can be seen, all of the text following the quote is extremely relevant, but was omitted in its entirety.
Out-0f date: Yes, but still relevant
- published 37 years ago, but on some fairly basic facts about thermodynamics.
This one is pretty clear, It's an extremely egregious selective quotation. In addition, the source citer is obviously wrong, as there is no such thing as the " Smithsonian Institute Journal" and few sites even attribute the quote properly to Asimov.

Marcsana's quote: The point is that in a non-isolated [open] system there exists a possibility for formation of ordered, low-entropy structures at sufficiently low temperatures. This ordering principle is responsible for the appearance of ordered structures such as crystals as well as for the phenomena of phase transitions. Unfortunately this principle cannot explain the formation of biological structures.
Purported to be from:
I. Prigogine, G. Nicolis and A. Babloyants, Physics Today 25(11):23 (1972)
References on creationist websites: 6. Example: Darwinism Refuted
Actually from: I. Prigogine, G. Nicolis and A. Babloyants, "Thermodynamics of Evolution (I)" Physics Today 25(11):23 (1972)
Actual quote:

The point is that in a non-isolated [open] system there exists a possibility for formation of ordered, low-entropy structures at sufficiently low temperatures. This ordering principle is responsible for the appearance of ordered structures such as crystals as well as for the phenomena of phase transitions.

Unfortunately this principle cannot explain the formation of biological structures.
The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred.

The conclusion to be drawn from this analysis is that the apparent contradiction between biological order and the laws of physics--in particular the second law of thermodynamics--cannot be resolved as long as we try to understand living systems by the methods of the familiar equilibrium statistical mechanics and equally familiar thermodynamics.

Selective quotation: Yes; note how carefully the creationists left out the actual title of the journal article! This two-article series, as detailed below, is actually an explanation of how evolution does not violate the Second law; part of the body of work that earned Ilya Prigogine the 1977 Nobel Prize in Chemistry. In addition, this quote is simply a prologue to Prigogine's explanation of how evolution is possible with non-equilibrium thermodynamics.
Out-0f date:
No. Although quite old, this research is still a valid explanation of how evolution does not contradict the Second Law.
The above quote explains how it is difficult to reconcile standard thermodynamic theory and evolution. Therefore, a different way of looking at the problem is needed. Prigogine proposed that "nonequilibrium thermodynamics describes how such systems come to terms with entropy." He described the theory of "dissipative structures" which are systems that lose (dissipate) heat while increasing order. Thus, in a non-equilibrium (open) system, such systems can be examples of increasing order, as they produce more entropy (heat dissipation) than the order that they gain, even as they become more orderly. As some examples, he gives patterns of convection in heated liquids and generation of light by lasers. There is much more to the theory than this, but it explains it in a nutshell without becoming too technical.

In specific regards to evolution, he states:
What is the thermodynamic meaning of prebiological evolution? Darwin's principle of "survival of the fittest" through natural selection can only apply once pre biological evolution has led to the formation of some primitive living beings. A new evolutionary principle, proposed recently by Manfred Eigen, would replace Darwin's idea in the context of prebiotic evolution. It amounts to optimizing a quantity measuring the faithfulness, or quality, of the macromolecules in reproducing themselves via template action. We here propose an alternative description of prebiological evolution. The main idea is the possibility that a prebiological system may evolve through a whole succession of transitions leading to a hierarchy of more and more complex and organized states. Such transitions can only arise in nonlinear systems that are maintained far from equilibrium; that is, beyond a certain critical threshold the steady-state regime becomes unstable and the system evolves to a new configuration. As a result, if the system is to be able to evolve through successive instabilities, a mechanism must be developed whereby each new transition favors further evolution by increasing the nonlinearity and the distance from equilibrium. One obvious mechanism is that each transition enables the system to increase the entropy production.

Marcsana's quote: As ice forms, energy (80 calories/gm) is liberated to the surroundings... The entropy change is negative because the thermal configuration entropy (or disorder) of water is greater than that of ice, which is a highly ordered crystal... It has often been argued by analogy to water crystallizing to ice that simple monomers may polymerize into complex molecules such as protein and DNA. The analogy is clearly inappropriate, however... The atomic bonding forces draw water molecules into an orderly crystalline array when the thermal agitation (or entropy driving force) is made sufficiently small by lowering the temperature. Organic monomers such as amino acids resist combining at all at any temperature, however, much less in some orderly arrangement.
Purported to be from:
C.B. Thaxton, W.L. Bradley, and R.L. Olsen, The Mystery of Life’s Origin: Reassessing Current Theories, Philosophical Library, New York, 1984, pp. 119-120.
References on creationist websites: 1. Example: True Origins
Actually from: Source is correct
Actual quote:
Presumably the same.
Authority of authors:
Authors are advocates of creationism/intelligent design. From the review mentioned below-"The authors are listed on the cover as PhDs in chemistry, materials science, or geochemistry. Not one is listed in American Men and Women of Science, 14th edition."
Selective quotation:
Out-0f date: Yes; book was published 23 years ago.
This is the one book I was unable to find; however, I found plenty of information about it. This quote is not from a scientific text. The quoted book was written by creationists.It received scathing reviews from scientists due to its extensive quote mining rather than presentation of any original work. As Dr. Sidney Fox, a professor at the Institute for Molecular and Cellular Evolution at the University of Miami, wrote in the journal The Quarterly Review of Biology:
Many of the negative criticisms consist of citing one "origin-of-lifer" vs. another; such literature is of course abundant in scientific journals in a frontier field. Although the presentation of such objections is thorough, a number of published rebuttals of statements conforming to the authors' thesis are not cited. For many readers the frequency of such omissions will raise thoughts about the ethics of such asymmetric scholarship.
So, in closing, in just these five quotes we have seen a wealth of selective quotation and misrepresentation. The prevalence of such shoddy scholarship in creationist works truly casts a very poor light on their efforts.

Thursday, August 16, 2007

No birdbrains here

I ran across this fascinating article today- BBC NEWS | Science/Nature | Cleverest crows opt for two tools.

It discusses the New Caledonian crow, a bird whose toolmaking and tool-using skills put even the great apes to shame. These clever birds recognize the need for a tool, then manufacture it in order to get the specific job done. They also realize which tools are best for which job. In the research described in the BBC article, the birds were presented with a short stick, a long stick in a cage, and a piece of meat in a Plexiglas box which could not be reached with the short stick. On the first trial, four out of six birds tested immediately picked up the short stick, used it to fish out the long stick, and then used the long stick to get the meat out of the box. There are incredible videos of the crows at work.

In other experiments, the crows bent wire into hooks that they used to retrieve small buckets of food from a pipe, and showed that they had a preference for using tools on one side or the other of their beaks.

In the wild, the birds fashion tools from the leaves of the pandanus (screw pine) tree, which have serrated edges. They carefully snip out sections of leaf- wide, narrow, or skillfully-crafted "stepped" tools that taper- and use them to extract grubs from holes. They also make hooked tools by whittling small branches- there is video of this process at the same link as above.

The videos are amazing not just for the skill of the birds, but their obvious attention to detail. In the film of the crows making hooked tools, we see them eye candidate twigs from every angle, then stop frequently while fashioning the hooks to check their progress. There is obviously much more going on here than simple instinct.

These crows are, of course, the object of much scientific study. One of the most intriguing theories being examined is the the crows have a toolmaking culture, where young crows have an inborn propensity for tool use which is developed by watching older crows. Older crows develop better tools and then pass the skill on to younger crows. Researchers believe that the "stepped" pandanus-leaf tools came about in this fashion.

Why are these crows so smart? Research is focusing on that now. It may be that the same evolutionary method is at work here as with keas- extreme generalization. It may also be that these crows are just good tool-users and not so smart in other areas. The researchers are hoping, as they put it, "to test between the adaptive specialisation and general intelligence accounts of the evolution of complex cognition." Studying crows may help us learn how we evolved intelligence as well.

Wednesday, August 8, 2007

News Flash! Common Garden Hose Shows The Earth is Really, Really Old!

Interviewer (yeah, really me, talking to myself) So what's all this then?

Cris: Well, I had this epiphany while watering my goats....

Interviewer: Um, does it involve any burning bushes or signs from Heaven?

Cris: No, nothing of that sort. You see, I turned on the hose, and it has a leak, you see. A little leak. I've tried to fix it, but it sprung another leak. It's had this leak for ages.

The hose in question

Interviewer: Okaaay...and this has what to do with geology?

Cris: Well, I live in Southern California. The ground is really, really hard here. Harder than lots of sedimentary rocks. So hard you need a backhoe to dig your garden. I could spend all day with a shovel and never get anywhere, certainly not to China.

Interviewer: That's a bit geological, then. Is there more?

Cris: Of course, we haven't even gotten to the best part! You see, the water comes out of the leak pretty slowly, and the hose is only on for 5-10 minutes at a time. But look at the canyon it's carved! I predict that, in 4.7 million years, if I let the hose trickle all the time, I could have the Grand Canyon in my backyard. But I think my husband would complain about the water bill.
Jamul Canyon

Wow, look at that steep bank!

The real Grand Canyon
Interviewer: That really does look a bit like the Grand Canyon in miniature. Why not just bring in a big tanker truck full of water and let it all loose here? Then you might at least have enough of a canyon to go whitewater rafting in.

Cris: I don't think that would work too well. I think if you dump out all the water at once, it won't carve a nice canyon. It will spread out over the ground and drain away. It might form some small channels, but not the Grand Canyon. Here, let's try it. OK, I have a large volume of water here, scientifically equal to the amount necessary to fill one empty Tidy Cat container. So here comes the deluge! Thunder and lightning please!
Experimental apparatus
The flood begins!
Aftermath of the flood

A closeup

Interviewer: Hmm, that doesn't look like the Grand Canyon at all, does it?

Cris: Not at all. It does look a bit like the area surrounding Mt. St. Helens, though.
Mt. St. Helens

Interviewer: That it does.

Cris: Well, I am just glad that a leaky old garden hose could give such an eloquent lesson in geology.