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Thursday, June 17, 2010

Book Review - The Tangled Bank

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

So ends Darwin's Origin of Species, giving the inspiration for the title of Carl Zimmer's latest book, The Tangled Bank: An Introduction to Evolution. It is described as a textbook on evolution for non-biology majors, and it is very good.

The term, 'evolution', is pretty broad. In general, when people talk of biological evolution, there are two broad categories they're referring to. The first is the concept of common descent with modification - that all life on this planet is related, and that populations of organisms change over time. The second is the theories describing how that works, with natural selection being the most famous. Pretty much every book that covers evolution will cover both areas to some extent, but often times they will focus on one area over the other. The Tangled Bank covers more of the latter subject. Of course, it uses examples, but it is more about how evolution works rather than a fossil by fossil account of the evidence for common descent (for that type of book, read Donald Prothero's Evolution: What the Fossils Say and Why It Matters - also, realize that there's much more evidence for evolution than just fossils).

Let me give an example of one of the concepts I learned about - Hardy-Weinberg Equilibrium. This term is probably familiar to biology majors, but it's not something us non-biologists generally read about in most popular books or magazine articles on evolution. The concept has to do with allele frequency. As a refresher, an allele is a variation of a gene. Think back to your high school biology class, and the genetic experiments of Gregor Mendel. For example, Mendel discovered a certain gene* that controlled pea color - one version would make them green, while the other would make them yellow. Each version is called an allele. Remember further, that us eukaryotes carry two copies of a gene (actualy, at least two - it can get a bit more complicated than this). So, individual plants in a population of all green peas might all carry two copies of the green allele - GG, and individual plants in a population of all yellow peas might all carry two copies of the yellow allele - YY. Now, if you were to bring those two populations together, the alleles woud start mixing, and you'd end up with three different combinations that the plants could have - GG, YY, and GY (GY and YG are the same thing). What Hardy-Weinberg equilibrium tells us, is that according to just random mating and chance distribution, these allele combinations should all be present in certain ratios. In this example, half of the plants would likely be GY, one quarter would be GG, and the remaining quarter would be YY. But what if you checked up on your pea population, and found that it didn't match the Hardy-Weinberg equilibrium? What if less than a quarter of the plants were GG, and more than a quarter were YY? Well, then we could conclude that something about the Y allele was advantageous to the plants, and that natural selection was pushing the population to have more plants with the Y allele.

This concept of Hardy Weingberg equilibrium can be applied to more complicated scenarios. It doesn't have to be just two alleles, and the initial distribution doesn't have to be 50/50. However, for any combination, the Hardy Weinberg equilibrium is the distribution you'd expect if there weren't any natural selection, and measuring how much the actual distribution varies from the Hardy Weingberg equilibrium is a measure of how strong the selection is.

To me, that's a pretty interesting concept, and it wasn't something I'd given much thought to before reading Zimmer's book. However, the book didn't go into much more detail than what I just gave in my summary. If you're not of a technical bent, that may be all you need. I realize that Zimmer's goal was to provide a book for non-biology majors, so maybe that's all the detail he felt was necessary. However, to someone like me, who may not be a biology major but wouldn't mind seeing a little light math, Zimmer's explanation was a little too superficial. I mean, if you follow that Wikipedia link I provided and read the explanation of Hardy Weinberg equilibrium, the math isn't all that hard. It's just a bit of algebra. Maybe as an engineer who works with equations all day long I'm a bit biased, but it's not as if you need to understand any calculus or differential equations to follow the basics of Hardy Weinberg equilibrium.

I can't discuss this book without mentioning the illustrations. Practically every page of the book has a figure or a graph. I'm sure that the printing cost associated with this contributed to the $50 price tag for the book, but it really makes it easy to understand certain concepts that would be difficult to get across with just words.

This book was published right around the same time as Richard Dawkins' The Greatest Show on Earth: The Evidence for Evolution, so there were inevitably comparisons. But the truth is that they're just not the same kinds of books. In my discussion above on the broad meanings of evolution, I said that Zimmer's book covered more the theories of evolution. Dawkins' book was more of a look at the evidence itself. Zimmer's book was a textbook with color illustrations on each page, while Dawkins' book was a popular book with few illustrations. Comparing the two is comparing apples to oranges.

If you'd like to get more of a taste of the book, I've found two excerpts available for download online. Chapter 1, Evolution: An Introduction is availabe from Carl Zimmer's own site. Chapter 10, Radiations and Extinctions is available from the National Center for Science Education. You can also read Zimmer's announcement of the book on his blog, to hear his intentions in his own words.

All in all, The Tangled Bank was very good. It was a nice broad introduction to many of the theories and mechanisms of evolution, but without getting too technical for those of us that don't plan to go into careers in biology. Unfortunately, being a textbook, it's a bit pricey. You may try going to your library to check it out, find it used, or maybe be lucky enough to be able to borrow it from a friend. However you manage to get your hands on a copy, I definitely recommend this book.

*Mendel's insight was that there were units of heredity, now known as genes, as opposed to the prevailing concept at the time of blending inheritance, but he didn't actually know the mechanism responsible. It wasn't until later that other scientists discovered that genes were contained on chromosomes, and later yet that scientists discovered that chromosomes were made of DNA.

Friday, June 11, 2010

A Skeptical Look at HHO Generators

A friend of mine sent me a link to an interesting device, known as an HHO Generator. HHO stands for 'hybrid hydrogen oxygen'. It's basically an electrolysis unit that runs off your car's electrical system, and sends the hydrogen and oxygen into the engine's air intake. The company selling the device claims gas mileage improvements on the order of 30% to 90%!

I'm skeptical. This seems too much like a perpetual motion machine. For example, you can't hook up an electric motor to an electric generator, and then have the generator power the motor. Resistance in the wires and friction in the moving parts will rob energy from the system and dissipate it as heat into the environment. In fact, if you just had a flywheel of the same inertia on low friction bearings, it would spin longer.

I drew up two quick diagrams to illustrate what I'm getting at with this HHO generator. The first diagram below is a normal car - it burns gasoline to power the engine to turn the wheels. Below that is a car with the HHO setup.

Energy Flow in Conventional Car

Energy Flow in Car with HHO Generator

That extra loop resembles a perpetual motion machine too much. You're taking energy from the engine to split water, then trying to use that as fuel to turn the engine, and hoping to get more energy out than you're putting in. But remember, there's friction in the alternator and resistance in the wires running from the alternator to the HHO generator; when you run current through the water, only some of it goes into splitting the molecules while the rest heats up the water; and then there's also friction in the lines from the HHO generator to the intake. You're losing energy to heat in every step of that process.

Still, my friend bought that system and installed it in his car, and he insists that he's getting better gas mileage than before. So, I've tried to think of reasons why this may be the case. Here are my thoughts.

1) The hydrogen makes the combustion process more efficient, so that the engine converts more thermal energy into kinetic energy. This really seems pretty unlikely, though, especially without doing any additional modifications to the engine. First of all, the increase in efficiency would have to more than offset all the lost energy from the HHO generator. And internal combustion engines are already really efficient, especially modern engines with oxygen sensors and fuel injection that can tailor the air fuel ratio. And automotive companies are under pressure from government regulations (not to mention market forces) to make the engines as efficient as possible. Given the number of engineers working on these engines, and the amount of money manufacturers spend on development, I can't imagine that there's much room for improvement in efficiency.

2) He hasn't done enough tests. Fuel mileage is strongly dependent on driving style and other variables. A lead foot burns a whole lot more fuel than driving conservatively. Sitting at stops signs and traffic lights hurts fuel economy (even though the engine's at idle, you're getting zero miles per gallon during those times). A head wind will hurt you, while a tail wind helps. Properly inflated tires have a noticeable effect. I don't think a few tanks of gas driving around town is enough to smooth out all those variables. You either need to do some really controlled testing (an external fuel tank you can weigh on a closed course), or run thousands of miles with and without the HHO generator for comparison.

3) The hydrogen and oxygen are messing up the oxygen sensors. Engines are usually tuned to run at lower power at a stoichiometric air fuel ratio (AFR). This is when the amount of gasoline and oxygen are matched up perfectly, so there's no fuel left unburnt, and no free oxygen left. However, as the engine's power output increases, if it continued to operate at the stoichiometric AFR, it would burn hot enough to damage engine components. That's why the AFR needs to be enrichened - the extra fuel lowers the combustion temperature, keeping the engine from getting damaged. I've got some first hand experience with that - at work, we hired an 'expert' consultant to help us tune an engine, and he let the exhaust gas temperatures (EGTs) get up to 1750ºF (we usually tried to keep them below 1550º), and it literally burnt the ends off of the spark plugs.

The other problem with running too lean is that the engine could start knocking (when the fuel air mixture explodes instead of burning smoothly). That's another reason the AFR gets enrichened. I've got some first hand experience with that, too. We were tuning the engine another time (at a different shop), and we had a laptop hooked up to the engine computer that gave us real time feedback on all the variables the engine computer was monitoring. We kept advancing the timing (another variable that strongly influences knocking) to try to get the engine operating as efficiently as possible. The guy operating the dyno had run plenty of engines, so he had a good ear for it. The laptop was telling us that the engine was sensing knocking, but the guy running the dyno couldn't hear it, so we figured it was a false signal. After a few more dyno runs, we basically destroyed the engine. When we took it apart and inspected it, it had all the signs of knocking. The moral being - your ear isn't sensitive enough to reliably detect knocking at levels that are still high enough to damage your engine.

If the hydrogen and oxygen are messing up the oxygen sensors, it may be tricking the computer into running the engine leaner. This would improve fuel economy, but at the cost of higher EGTs and increased chance of knocking - both of which will reduce the life of your engine. Unfortunately, there's no way of telling on a more or less stock system. Block temperature is not a reliable indicator of exhaust temperature, because there's plenty of capacity in the cooling system to keep the block temperature low enough. And knocking isn't something you can always catch by ear.

My gut feel is that it's probably option two above. I think that with more testing, my friend will find that the HHO generator is actually hurting his gas mileage. If it turns out to be option three, though, it could be causing some serious damage to the engine. I recommended to him that he at least pull the plugs periodically to see what they look like, and that it might not be a bad idea to invest in some EGT probes and a knock sensor, either.

Anyway, after a little bit of research, I did find a few other sites discussing this (the first link below is the best). It looks like my second option above is the most likely.

It looks like maybe there could be something to these HHO generators in an engine specifically designed for them, but nowhere near as much as many of the scam artists are claiming. Plus it's analagous to octane. High octane fuel doesn't explode as easily, so some of those things that cause knocking (advanced timing & leaner mixture which I already discussed, plus higher compression ratios which I didn't mention) can be pushed harder if you have high octane fuel. So, if you have an engine designed to take advantage of high octane fuel, you can get better efficiencies. But, if you simply run high octane fuel in an engine designed for low octanes, you won't see any difference. Some of the stuff I've seen for hydrogen says that it might allow you to run leaner than with pure gasoline, but your engine and sensors would have to be designed accordingly. Simply pumping it into a stock engine wouldn't give you those benefits.

Thursday, June 10, 2010

Done Arguing

The comment thread I was arguing in over at The Chronicle of Higher Education is now officially done. Commenting has been closed, so there's no chance of adding anything new. Since I've copied all my other comments from that thread into previous entries on this blog, I figured that for the sake of completeness, I'd include the last of them here. Again, since this is reposting information instead of posting something original, I'm putting it all below the fold.

For reference, the previous entries where I posted comments from this thread are available here:
Arguing About Religion On Another Site
Still Arguing


Your explanation was good overall, but I do have a few nits to pick.

"Intelligent design provides no non-supernatural mechanism to support how life was created and evolved on this Earth. Again, it must be dismissed for that reason alone as being not science and anyone who desires to teach it in the classroom as science must be stopped (though dismissing them from their jobs, is, admittedly, going too far)."

People get hung up here on the natural vs. supernatural distinction. Science just requires evidence. If there were evidence to support the creation story in the Bible, then science would lead us to accepting that story. In fact, prior to Darwin and Wallace, special creation was the dominant scientific theory for the origin of life. It was the stronger evidence for evolution over creationism that lead scientists to accept it as the better answer.

"anyone who desires to teach it [ID] in the classroom as science must be stopped (though dismissing them from their jobs, is, admittedly, going too far)."

For a first offence, maybe, but why is it going too far to fire teachers who teach students false information? What if an elementary teacher taught students that 2+2=5? Or if a history teach taught that the moon landing was a hoax? Teachers have a responsibility to teach students true information, and they have no business being teachers if they intentionally teach students falsehoods.

Professors have the freedom to research ID all they want, just not to teach it to their students.

Also, sammy_ayers was referencing Expelled, which to be frank, lied about actual events to portray people as being harassed for discussing ID. I included a link to my own blog about Expelled above, but two better places to read full rebuttals to the claims of harassment are given below.

Re: Religion

Zagros, your arguments for 'mere belief' so far haven't convinced me. There may not be an infinite number of gods that people have believed in, but there are enough, with mutually contradictory attributes, that it makes Pascal's Wager break down. If the commonly accepted view of Christianity is correct, it does you no good to believe in a deistic god but to not accept Jesus. You'd still go to hell (similar arguments apply to Islam, or Zoroastrianism). You can argue that you don't believe Yahweh is like that, but your personal opinion makes no difference to objective reality. So, it does you no good to just believe what you want to be true. You have to do your best to determine what is actually true. (I've heard the elephant story before. My same objections still apply. It's fine if a god is nice and forgiving and gives you an A for effort. It's worthless if the god is vindictive and punishes you for not following a specific scripture. Besides, if the elephant story is true, I'm in no danger as an atheist as long as I live a good life and try my best to do good in the world.)

The other problem with Pascal's Wager, which you alluded to yourself, is the argument that belief in the absence of a deity costs you nothing. That's clearly not the case. If you actually attempt to determine a deity's wishes, there are some clear instructions on how to live your life. In the case of the Abrahamic religions, some of these seem to make no sense (no mixed fibers, not eating shellfish, not being able to work on a specific day of the week, no homosexual relations). These do have actual, real consequences on our lives, so why should we even attempt to follow these rules if they're based on an imaginary being, or on a being with a very low probability of existence?

Your definition of a strong atheist is different from what most of us who call ourselves strong atheists actually use. As you pointed out, Richard Dawkins, who I'm sure most would refer to as a strong atheist, conceded a tiny possibility that a god exists. (When pressed, we'd also admit a small probability that Last Thursdayism is true, or that The Matrix was a documentary. We can't rule out those possibilities entirely, but we can say that the odds are so small that we're pretty sure they're false.)

You wrote, "There clearly is a larger 'weight of evidence' in support of a supernatural creator of the universe (God) but that is not science and can never be science for the reasons thus explained." What weight of evidence are you referring to? We don't know what caused the big bang, so what good reason is there to assume that it was supernatural? More importantly, what reason is there to assume that it was intelligent (and if your definition of a deity says that it need not be intelligent, then why even call this concept a 'god')?

Re: Evolution

Zagros, you're trying to neuter science. In your definition of science, if special creation did actually happen, we couldn't use science to study it. To disqualify potential real world events from scientific study is absurd. As I said before, we can use science to study anything that leaves evidence. If there were evidence for special creation, we could study it with science. If miracles happened, they could be observed and documented. Even things traditionally classified as supernatural, such as fairies, could be studied by science if they actually existed (look at the fraudulent photos that fooled Arthur Conan Doyle). Way back up in this thread, new_theologian listed some supposedly miraculous occurrences he thought were evidence for the divine, and I responded with ways that the miracles could be studied scientifically. The only things we can't study with science are those things that leave no evidence, or in other words, those things that don't interact with our universe. A deistic god who set everything in motion at the start of the universe but then remained hands off for the rest of eternity fits this description, but not the interventionist type god required by Intelligent Design.

Let me touch briefly on what Intelligent Design actually is, since I think that would clear up some of the confusion here. ID advocates are usually pretty vague on what ID actually entails, but here are a couple quotes from Of Pandas and People, the ID textbook that was going to be used in Dover.

First, in discussing tetrapod evolution on page 22, the book said, "Instead, fossil types are fully formed and functional when they first appear in the fossil record. For example, we don't find creatures that are partly fish and partly something else, leading gradually, in the dozens of characteristics which they exhibit, to today's fish. Instead, fish have all the characteristics of today's fish from the earliest known fish fossils, reptiles in the record have all the characteristics of present-day reptiles, and so on."

In discussing the incompleteness of the fossil record on page 25, the book said, "There is, however, another possibility science leaves open to us, one based on sound inferences from the experience of our senses. It is the possibility that an intelligent cause made fully-formed and functional creatures, which later left their traces in the rocks."

The main difference between Intelligent Design and creationism seems to be that ID doesn't specify who the creator actually is, and leaves open the possibility that Earth is one giant lab experiment for advanced aliens (without specifying how the aliens themselves came into existence). If you accept evolution but believe that a god was involved in the process, there are other terms that better match your position. 'Theistic evolution' accepts that evolution has happened largely as the scientific theories predict, but that a god has been imperceptibly tweaking the process to ensure its desired outcomes. 'Front loading' accepts that a god created the universe with the right conditions from the outset to result in its desired outcomes, but that the god hasn't directly intervened since. This may all be semantics, but I think it's relevant to this conversation.

Re: Origins of Life

sammy_ayers wrote, "If cell bootstrapping has happened in the past, why isn't it still happening now? Why can't we find a single example, anywhere? Why would it have happened in the past yet is no longer happening?"

For the same reason it's hard for a start up business in an established market - competition. The first life had no competition. It could afford to be inefficient and have a lousy metabolism. But life has had 4 billion years of competition to hone us into pretty efficient organisms. First of all, any free floating proteins and amino acids that could be used as building blocks for new life are likely going to be consumed up almost immediately by bacteria or protozoa. Even if given a chance to come together, any incipient life forms on Earth now would themselves probably be gobbled up almost immediately by bacteria or protozoa, or at the very least be out-competed.

Re: missing links

There's an old joke about missing links. When a scientist finds a fossil that fits into a previous gap, a creationist says, 'Well now you've just made the problem worse. Instead of only one gap, now you have two.'

Fossilization is rare. We don't have fossils of all living animals, so why should we expect to have fossils for all extinct animals? Look at it this way, if you could trace your ancestry back several generations, but couldn't find any record of your great great great grandmother, would you assume that she didn't exist, or that you simply couldn't find the records?

That being said, there are some remarkable transitional fossils. I've already recommended Donald Prothero's Evolution: What the Fossils Say and Why It Matters, which is full of fossils. To list just a few here, Archeopteryx is probably the most famous, clearly having traits of both living birds and its non-avian theropod ancestors. There's the recently discovered Tiktaalik Roseae, which has been dubbed a fishibian. There are Pakicetus and Ambulocetus showing whale transitionals.

But this whole focus on 'missing links' misses the point. It's the overall story that paints the picture, not isolated fossils. For example, Tiktaalik on its own would be interesting. But it's when you compare it to other organisms like Eusthenopteron, Panderichthys, Ichthyostega, and Acanthostega, that you begin to better understand the evolution of tetrapods.

Re: human evolution

sammy_ayers wrote, "Why are there no apes today that exist in various stages of mutation into man?"

Why should there be? There is no ladder of progress. Humans are no better or worse than the other apes. We're adapted to our environment. The other apes live in different environments, so there's no pressure to make them adapt to be like us.

sammy_ayers also wrote, "Despite the huge amount of money the finding would be worth :-) there is no scientific evidence that man decended from apes."

I would disagree strongly. There's both strong fossil evidence and genetic evidence. In fact, there's too much to list here, so I'll recommend two good places as starting points:

zagros wrote, "It has been proven that man was not descended from apes."

I understand what you're getting at, but this is one of my pet peeves. It would be like saying blue jays aren't descended from birds. Of course we're descended from apes because we are apes ourselves. You can't possibly classify chimps and gorillas as apes without including humans, since chimps are more closely related to us than to gorillas. I imagine that you meant that humans are not descended from any living apes, but I'm pretty sure that if we got in a time machine and traveled back 6 million years to find our ancestors, we wouldn't hesitate to call those creatures apes.

Re: sammy_ayers Questions:

"Do you believe educators should be punished for mentioning intelligent design within hypotheses and theories published to the scientific community?"

It depends. If it's taught in the same way as the aether theory of light, or the law of recapitulation, then there's nothing wrong with mentioning ID. If it's presented as credible science, then the teachers should be punished.

"Do you believe that intelligent design should be ommitted from textbooks and classrooms while other, less likely hypotheses and theories are included within text books and classrooms?"

Unless presented as above, ID should be omitted, and less likely explanations should definitely be omitted. However, evolution and current thoughts on abiogenesis are much more likely than Intelligent Design.

"Do you believe that hypotheses and theories regarding intelligent design should receive less public resources and funding than equally unproven and potentially less likely hypothesis and theories?"

As soon as someone can present a testable theory for ID, I wouldn't mind a little taxpayer money going to test it. But what are these "equally unproven and potentially less likely hypothesis and theories" that you're referring to? Because as I already said, evolution itself is pretty much a fact, and current thoughts on abiogenesis are much more likely than Intelligent Design.

This isn't one of your three questions, but it's close. You wrote, "...you believe we taxpayers who are paying for public schools and universities, should simply overlook the fact that our children are exposed to every hypothesis and theory regarding the origins of life, except that the possibility that life originated by intelligent design will be expressly not permitted."

First of all, children aren't exposed to "every hypothesis and theory regarding the origins of life". They're only taught the most credible ones. Regarding Intelligent Design, I disagree with zagros here. If there were any evidence for intelligent design, I think it would be a fruitful area for research. I wouldn't exclude it a priori just because it may have to do with a deity or may have religious implications. The problem is that the evidence just doesn't exist. That's why it's not suitable to teach to children.

Re: Talk Origins

sammy_ayers, I've already mentioned this to you twice, but I'll mention it a third time. I'd highly recommend that you peruse the Talk Origins website. I'd especially recommend that you browse their Index to Creationist Claims before posting anything further about evolution on this thread. Many of the erroneous arguments that you've picked up from dishonest sources are refuted on that page.

Sammy_ayers and zagros both left responses. If you're interested in reading them, head on over to the original thread.

Friday, June 4, 2010

Still Arguing

Well, I don't have any new entries this week, either. I got too caught up in that same comment thread on The Chronicle of Higher Education as last week, and spent too much time leaving comments there. I think I'm suffering from SIWOTI Syndrome. Like last week, if you're really interested in reading something by me this week, I've included my comments below the fold.

For reference, the previous entry where I posted comments from this thread is available here:
Arguing About Religion On Another Site


I didn't get a chance to respond before the 3 day weekend, so here's my late response now.

I don't want to belabor the point on stealing, but you still haven't really responded to it satisfactorily. You've called it a moral imperative, but don't provide any justification for why. I may be swayed by your argument, but you haven't presented one, yet.

The other examples you listed can be accounted for by maximizing good/minimizing harm. You stated that "downloading music off the Internet will not harm the original musician and that is especially true if you would never have paid for the music under any circumstances." Pirated downloads are lost revenue for the musician/company. That's why it's stealing, and why it's morally wrong. If you wouldn't have actually paid to listen to it if it wasn't available for free, that does make it a bit more like the armageddon stealing scenario you invented above, but I don't think it's quite the same, especially in the real world. Why would you take the time to download the song if you didn't have some interest in it? And if you do have some interest in it, then you're really just trying to get out of paying.

Cheating also causes harm. Aside from the breach of trust during the test itself, you are now misrepresenting yourself to future employers, who have an expectation that your grades represent a certain mastery of material. You are also hurting fellow students by cheapening the degree (if this guy got a B from such and such university and has such a piss poor understanding of the material, why should I hire this other guy from that school who got the same grades?)

You've stated several times that the existence of gods is an opinion. This may be semantics, but I disagree. Gods either exist or they don't. It's a fact one way or the other. We may not be able to reliably determine the truth, but that doesn't make it an opinion.

You've also stated, that if two people have the same moral system, and the only difference between them is that one believes in a judgmental god while the other doesn't, then the believer will probably behave better because of the incentives. I guess I finally see your point, but when does this actually apply? This is similar to what Gowexo said in comment 177, but if a person believes in a judgmental deity, they don't get to pick any old moral system that they want. They can't just say that they personally think an action is right or wrong. They have to go by what the deity will reward or punish for. This is why I brought up the 'opinion' point above. We don't define reality with wishful thinking. If a deity did exist, and if the deity did reward and punish certain actions, then we ought to try to truly understand the deity's criteria for judgment.

Of course, it goes without saying (and I'm not saying this is your position, just clarifying for anyone else still following this thread), that whether or not belief in a deity makes people behave better or worse says nothing about the actual existence of the deity. Children may behave better around Christmas time because of their belief in Santa Claus, but it doesn't make Santa any more real.

Several times, you've said something to the effect that a god can neither be proven nor disproven, so it's perfectly reasonable to believe in a particular god (in your case, Yahweh). From your response to people bringing up the FSM (which was originally intended as a mockery of teaching Intelligent Design in schools, not necessarily religion in general), I take it you don't think Russell's Teapot is a good example of why lack of evidence is a good reason to doubt the existence of something. So, I'm curious about your take on other mythological beings, like fairies and leprechauns. These are not inventions intended to make religion look silly, but things many people have sincerely believed in. Since they're magical creatures, similar arguments that people use for gods can be made about why there's no strong evidence for them (they can use their magic to hide themselves, make the evidence disappear, etc). Do you take a similar agnostic stance on their existence, or do you dismiss these beings as products of our imagination? If you do dismiss them as imaginary, what is your justification for the different treatment of a deity?


zagros already responded to your post pretty well, but I'll add to it. You wrote, "based on the evidence and the numbers that I have seen, it seems that one must have as much faith to believe that life formed from a primordial soup, as to believe that life was formed by the result of an intelligent design, i.e. by a creator."

Concerning the faith part, and assuming that you're talking strictly about abiogenesis (not evolution), I can almost see your point. We don't know exactly how life got started on this planet. However, I wouldn't call it faith to expect that we'll discover a non-supernatural explanation for it, any more so than I'd call it faith to expect that politicians will lie in the next round of campaigning. I can't see into the future, so I can't say with 100% absolute certainty that future politicians will lie, but given their past performance, I'd say it's a pretty safe bet. Similarly for the history of this planet, we have a decent idea of how it was formed naturally over 4 billion years ago, and we have a really good understanding of how the life on it evolved naturally from several billion years ago to the present. There's a gap in our understanding between the formation of the planet and once life was already going strong and evolving, but I don't see any reason to jump to expecting that a supernatural cause will be required to explain that period, especially if you consider everything zagros wrote about in his response to you.

I don't doubt your sincerity when you wrote that you doubted abiogenesis "based on the evidence and the numbers that [you] have seen", but I'd wager that's because of how poorly evolution and abiogensis are taught in many schools, and how many anti-science organizations there are that spread misinformation (such as Answers in Genesis or the Discovery Institute). The Talk Origins website is a great place to learn about this, along with rebuttals to many of the common anti-science arguments. A couple of really good books that discuss evolution in general and touch a bit on abiogenesis are Evolution: What the Fossils Say and Why It Matters by Donald Prothero, and The Tangled Bank: An Introduction to Evolution by Carl Zimmer. The former focuses mostly on the fossil evidence for universal common descent, while the latter is more of an explanation for the theories describing evolution.


I'm sorry. I hit the submit button before refreshing one more time and seeing your latest comment. Your comment at 201 seems to be implying that you think the intelligent designer was non-supernatural, while in my response I assumed you meant a supernatural intelligent designer. After thinking about it a bit, though, I don't think there's much to change. We still understand the formation of the planet and the subsequent evolution of life without needing to invoke an outside intelligence, whether it's a deity or advanced aliens. I don't think there's any reason to suspect that the initial start of life required an outside intelligence, either.


Regarding your arguments from authority for ID, zagros has already provided a link to Richard Dawkins' own site showing that Dawkins doesn't support ID. The 'documentary' you've cited, Expelled, is really little more than propaganda. The interview with Dawkins was edited dishonestly in such a way as to misrepresent his actual position. I've already written a review of Expelled on my own blog, if you're interested in reading more of my opinion of the movie, but I won't go on about it here.

You also cited Isaac Newton as a supporter of Intelligent Design. As Zagros already pointed out - who cares? Newton died in 1727, while Darwin and Wallace didn't publicly present the theory of natural selection until 1858. Newton may have been a genius, but he was limited to the knowledge of his time. Besides, would you use Newton's belief in alchemy to suggest that the Philosopher's Stone is real and can change lead into gold?

You wrote, "Regarding entropy, since no one is able to actually place a bound on the size of the universe (and as some believe there are universes outside our universe), how can one possibly establish the definition of a "closed system"? But where does one draw the boundary for a closed system when the universe is at the same time both infinite and infinitesimal?"

Defining open and closed systems is something people do all the time. We can't model the entire universe every time we want to calculate how different things interact, so we have to define a system that covers just enough to accurately predict what we're interested in. Defining the system is largely a matter of convenience and what makes sense. For example, if you were interested in the short term heat transfer between an ice cube and water in a well insulated thermos, you could reasonably approximate that as a closed system, because heat transfer to the outside world would have a negligible impact on what actually happens. However, if you're interested in studying something like global climate, and you want to define your system as just the Earth and it's atmosphere, you'd have to define it as an open system, to account for the energy coming in from the Sun, and the energy being radiated off into space. If you expanded your system further to the solar system, then you probably could make it a closed system.

So, as far as evolution is concerned, there's no problem in how you define the systems. If you look at the solar system as a closed system, any local decrease in entropy on Earth is more than made up for by the increase of entropy in the sun. On a smaller scale, if you treat an organism as an open system, any local decrease in entropy in the organism's gametes (which is where the raw material for natural selection comes from, after all), is accounted for by the energy the organism gets from food. Look at it another way. If the second law of thermodynamics said there could never be any local decreases of entropy ever, it would be impossible for any of us to exist, since we grew from single cells into full adults, which definitely required a decrease in entropy to organize all the raw materials into us.

You went on to write, "The fact is, entropy does not seem to be a law at all. It is more, as I put it, a 'pattern'. "

Of course entropy is not a law. It's a property of matter. Just like gravity isn't a law, but a force. Law's are what describe these phenomena. The second law of thermodynamics describes entropy, and it has been backed up experimentally over and over again.

I've written more about entropy on my own blog, as well, if you're interested in reading more of what I've said about that.

On the topic of scientists being close minded to intelligent design because they want to deny a creator, I'll quote a section of that review of Expelled that I linked to above. "Science of any stripe is secular, not atheistic. Meteorology predicts weather without resorting to divine intervention, and the germ theory of disease doesn't include demonic possession. Yet most people don't accuse those branches of science as being atheistic. Why, when looking at how life changes over time, is it all of a sudden atheistic to describe it naturally? It's not. It's just following the evidence."


I have one more question. In one of my previous comments, I mentioned a few good resources for understanding evolution. I don't expect that you'd rush off to the bookstore or library based on a suggestion from a stranger, but have you bothered to look at the Talk Origins website? It really is pretty good, especially at addressing the misconceptions and misinformation that abound regarding evolution.

Follow Up: I've reposted the rest of my comments from this comment thread.
Done Arguing

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