Science: The Missing Manuals

There's a series of O'Reilly books called "The Missing Manuals." We need something like that for science writ large to help address claims of the denialists.



Use "Evolution" as the paradigm. There are different kinds of science sites about evolution. NCSE keeps us informed about the latest happenings - upcoming talks, recently published items in the popular press, court cases, etc. Understanding Evolution at Berkeley is one of several great sites that explains evolution. But a very important website is talk.origins that started out as a Usenet group. TalkOrigins gives the canonical list of refutations of creationist pseudo-arguments. Why is that important? Because creationists flood the "marketplace of ideas" with false facts, poor reasoning, etc. The impression on the unwary is that they must have something important to say, because so many people are saying it. TalkOrigins systematically examines nearly every claim that creationists have made - and while they are not peer-reviewed, most of their articles have citations to primary literature.

Of course there are other sources of good and important information: Blogs like Pharyngula, or The Panda's Thumb are invaluable for giving in-depth analysis and background information.

Additionally, sites like Darwin Online has made the complete works of Darwin available to the entire world. Frank Lambert's site on thermodynamics examines and explains that subject in
clear detail for the layman.

These are all great sites, but TalkOrigins is an ace in the hole. The entire case for creationism depends on a thorough misrepresentation of the facts, laws, theories, history, methods, and philosophy of science. And TalkOrigins addresses those misrepresentations head on.

I think this kind of paradigm could be useful to address other kinds of denialism - in particular, HIV/AIDS denialism, anti-vaccination, anti-Global Warming and perhaps others. Probably these should be individual sites - and not one big denialist-refutation site. But the details are unimportant at this point. What's important is the recognition that such sites can serve a unique function. They are not complete solutions. They are not perfect solutions. But they are very important pieces to a solution. And their contribution is different than that of blogs, etc.

Now, I'm not the guy to actually build a site like this. But we ought to acknowledge that such a thing could be helpful OR explain why these other situations are sufficiently different that an analog to TalkOrigins would not help. And there are crucial differences - for example, the anti-vaccination groups are much more prone to inducing hysteria than the evolution-deniers.
But so far, I can't think of any good reasons not to have such a site - and some very good reasons for having them. What do you think? If you think, it would be helpful, take the idea and run with it - or talk it up. The canonical list of refutations of denialist arguments for X could be a boon for the community of non science-deniers.

The Second Law of Thermodynamics Refutes Evolution

Students of Kent Hovind understand thermodynamics better than any other humans. They explain clearly that the second law (hereinafter referred to as 2LOT) refutes evolution, because the second law says that everything tends towards disorder, but evolution is a process that increases order. This is a thoroughly damning argument and all the scientists of the world should feel deeply ashamed of themselves for overlooking the consequences of such an obvious and fundamental law on their theory.

Let's clarify the depth of scientific depravity exhibited by these EVILutionists. 2LOT requiresw that entropy must increase. Entropy is a measure of disorder. Therefore, 2LOT is a statment that disorder must increase. Let's look at a definition of second law from the scientists. There are several statements of 2LOT and while they are all equivalent, we should pick one that talks explicitly about entropy, so we can be sure that we understand how it relates to this devastating creationist argument.

According to the Division of Chemistry Education at Purdue:

"Second Law: In an isolated system, natural processes are spontaneous when they lead to an increase in disorder, or entropy."

A more common way of saying this is "In an isolated system, Entropy cannot decrease." But what is an isolated system? An isolated system is one in which neither matter nor energy are exchanged with the surroundings (of the system). So, this is a system that is not "connected to" anything else. In this sense our intuition of the term isolated corresponds fairly closely to the scientific denotation.

Dr Hovind's students inform us that entropy is a disorder. Is that correct? Not quite. The world order has a very specific meaning here. Thermodynamic order refers to the availability of energy for doing work. Recall the first law says that energy cannot be created or destroyed. 2LOT says that the even though energy is not destroyed, it can still become unavailable for doing work. Modern chemistry texts are beginning to eliminate the use of the words order and disorder altogether to describe entropy. Thanks to the efforts of Dr. Frank Lambert, university chemistry texts are giving more rigorous (and correct) explanations of the concept. Dr. Lambert is unambiguous in his criticism of equating entropy with disorder . Here's a sample:

"Shuffled Cards, Messy Desks, and Disorderly Dorm Rooms — Examples of Entropy Increase? Nonsense!"

from the Journal of Chemical Education, Vol. 76, pp. 1385-1387, October 1999."

If that were not sufficiently clear, Dr. Lambert further explains "Changes in the arrangement of ordinary objects do not change their entropy. Entropy depends on the dispersal of energy at a specific temperature, not on a pattern."

Entropy is not at all about disorder in the way that people commonly think. It's about the dispersal of energy; that is, it's a measure of the energy in a system that is no longer available to do work.

Of course, it's incredible to suggest that Dr. Hovind could be wrong about this. Let's go on, though. Again, 2LOT says the entropy of an isolated system cannot increase. The Earth, however, is not an isolated system. It gets matter in the form of space debris and it gets massive amounts of energy from the sun. So the basic premise for applying this definition to the biological evolution on Earth is not correct.

Hovind acolytes respond with quotes from scientists who assert that the second law applies to all systems. Those scientists may be correct, but their comments are irrelevant and misapplied. There may be definitions of the 2LOT that apply to other kinds of systems, but the particular statement of 2LOT that they are attempting to employ specifically states that it applies only to isolated systems. The definition itself says that it applies to isolated systems!

How is this possible? The entropy locally (on Earth) decreases at the expense of creating greater entropy in the universe at large!

Hovind and his standard bearers help us explain this by noting that, yes, while entropy CAN decrease in a system, that there must be some kind of engine for this to happen. But they are referring to a phantasmal definition of 2LOT in this case - one that exists only in their own minds, because 2LOT makers no mention of such an engine. That isn't what 2LOT says and that isn't what 2LOT means.

Tragically, Hovind has no better understanding of the second law of thermodynamics than he does of the first. This is unsurprising, because he is not a scientist and has never been a scientist; nor does he have any particular understanding of science. And here's a scary thought. One of Dr Hovind's great bragging points it that he taught high school science for 15 years. With such a poor understanding of actual science, one wonders what he could possibly have had to teach his students on the subject. Here's a problem - in some cases, any idiot can call himself a teacher and start "instructing" students. In the same way any deluded imbecile can make YouTube videos. Tragically Hovind has apparently instructed his own son, Eric, who seems to be following in his father's ignorant footsteps.

The Laws of Thermodynamics Refute Evolution


Kent Hovind and his devotees know, of course, vastly more about thermodynamics than the people who have studied it, and teach it, and write books about it, and apply in their jobs to solve real-world problems or provide insight into scientific investigations.

I would sooner consult Hovind for tax advice than science advice, but that, of course, is my materialistic bias speaking. His followers know The Truth, namely that Evolution is refuted by the first and second laws of thermodynamics (1LOT and 2LOT).

How so? The first law says that matter can't be created out of nothing. And since evolution does not explain where matter came from, it must be wrong. As my nemesis Edward Current would say, "Checkmate, Evolutionists!"

Also the second law states that everything tends to disorder. Since evolution means things are getting getting more orderly and more complex, it violates this law. Once again, evolution does not fair well.

Okay! We're done! The scientists can go home 'cause Hovind and his bleeting flock have figured it all out and have carefully articulated it to the layman. Thanks, Kent! I'm convinced!

Let's see if this reasoning checks out, though. Just a formality.

Regarding 1LOT, Kent has really nailed it. The evolutionist scientists are probably peeing their pants right about now. Biological evolution does not explain where matter came from. Nor will it ever explain where matter came from. Of course, explaining where matter came from was not the intent of those who formulated evolutionary theory. How could they have overlooked this obvious fact? Probably they were trying to pull a fast one! On the other hand, what about atomic theory, germ theory of disease, relativity, maxwell's equations, Boyle's law? None of those things explains where matter comes from either! Are those theories and laws also false because they don't explain where matter came from? Are they bad theories? Well, either they ARE bad theories, in which case all of science needs an overhaul, OR it could be that Kent has made an implicit assumption about what theories are and what they are supposed to do that isn't quite correct.

Does a theory have to explain everything? How many theories do you know of that explain everything? When Kent's minions point out, correctly, that evolution doesn't explain the origin of matter and energy, it's not any more relevant than the fact that Newton's laws don't explain the origin of matter or the first law itself doesn't explain the origin of matter.

No theory has to explain everything. No law has to describe everything. Creationists who spend even a few moments in reflection will realize this. It isn't the scientists who have misrepresented the facts in this case. It's Kent Hovind, the non-scientist, and Kent's zealous followers who keep repeating the same uninformed claim, despite the fact that it's nonsensical, who are misrepresenting the facts.

In summary, while evolution does not explain the origin of matter (or energy), there is no reason to expect it should. It's a bizarre and inconsistent way of thinking to insist that evolution must or ought to explain the origin of matter.

Creationism: Are all PhDs created Equal

Semi-transcript of my latest vid:

So I got mail from a creationist the other day. I don’t know to which of my videos he was responding, but he said something along the lines that 1000s of scientists were converting to 6 day creationism and gave me a link to statements by 50 of them at creation ministries who believed in literal 6 day creationism. I suppose he thought I would just bend over and drop trow.

But there was something immediately curious about the thing. Several of the 50 weren’t scientists – they was a geographer, several engineers, a few doctors, and one guy among the first 2 or 3 on the list who didn’t even have his PhD from an accredited school! Several of the others were associated with a particular religious school. When I pointed this out and compared them to “real experts,” the fellow as expected responded that I was closed minded because I didn’t consider his experts as real experts.

Okay. Let’s completely toss out creationism and evolution for a minute. I’m going to tell you about a few people I have actually known and a few experiences I have actually had. First, I took 2 courses from a guy who was considered (not by scientists), but by local authorities to be an expert in chemistry. This guy was the department chairman, had written a few papers, and had gotten a few awards. But I had him for 2 semesters and in all that time he was never ever – even one time – able to solve a single problem in class. He attempted nearly ever class, but could never quite manage it. It was mind-boggling.

Second, I knew a guy – I worked for him – who had a PhD in mathematics from perhaps the most prestigious university for that subject in the world. Certainly, it would be on everyone’s top 10 list. He was indeed a smart guy who knew very well how to manage projects and put together teams, etc. But one day we were working late and he started arguing with me over a piece of code. It was this huge program (order of a million lines of code) and he wanted me to go in and change the velocity of a particular thing. We were looking at the code and he told me to change this matrix…I said, “Uh…that’s a matrix… velocity is a vector … that looks like a rotation matrix.” To which he responded to me as if I were a complete idiot, “Velocity isn’t a vector.” Okay, I’m not going to go into a lot here. This guy really was very smart at a number of things – it’s just that calculus wasn’t among them.

Neither of these has anything whatsoever to do with Creationism or Evolution, but they illustrate an important point. A person isn’t an “expert” just because they have PhDs or are department chairmen or win awards. They’re not even experts if they write papers on things. So how then can you tell if a person is an expert?

Well, if the person has published peer-reviewed papers on the subject he’s writing about, then he might be an expert on that subject. It’s easy to check that kind of thing these days. There’s a service called EBSCOHost (among others) that allows you to look up every paper the person has published and even find out how many times it’s been cited in other works. That’s a good thing to know. What has the person actually contributed to the subject seems like a natural thing to ask.

So back to creationism, I was looking briefly at this fellows list of 50 and it was really weird – one of the guys gave Henry Morris’ book on young earth creationism as an example of a well-researched book that promoted creationism. Nobody who is actually familiar with this book and with science would say anything this stupid. Another fellow talked about how he believes because of what the Bible says and would believe regardless of any scientific evidence to the contrary. One of the scientists was Werner Gitt who wrote a creationist book on information theory claiming that it supports creationism. This is considered pseudoscience by those who are familiar with information theory.

It’s very strange. I have no idea how many times people on the net have tried to tell me what ‘real science’ who were theologians or poly sci majors or used car salesmen. Not a lot of them were well-versed in science, but most of them eventually get around to talking about all the PhD “SCIENTISTS” who believes in creationism, as if that fact alone should be sufficient to scare me into believing they might have a point. They apparently think that because they don’t understand the various subjects that no one else can either. The ideas of these creationist PhDs just MUST be considered legitimate science, because these guys are legitimate scientists. We’ll ignore for the moment the guy who doesn’t have his degree from an accredited university. Just because the others have PhDs doesn’t make them experts in the fields about which they’re pontificating. In fact, it was clear from their own words that some of them were just amateurs in the subjects that convinced them of 6 day creationism. Not all PhDs are created equal. Contrary to what this fellow and others said, I don’t reject a scientist’s opinion just because he disagrees with me even though that’s exactly what THEY themselves do. That’s why they ascribe this character to me – because they themselves posses it! No, what I maintain is that various people who are called experts aren’t experts just because they claim to be experts or because they wrote a bunch of religious manifestos on a particular subject.

Another of his “scientists” admitted he was not taught how to do science or what science was in university and he had to figure this out later. He then goes on to give a completely foolish view of what science is. “Science is about what can be observed…” I’ve addressed this in previous videos, but I might make one or even a series just about this subject.

My emailer also used AiG as a link which I thought was amusing. The planetarium of their new creation museum is run by a PhD named Jason Lisle who said that the difference between creationists and evolutionists is that creationists assumed the bible is true and evolutionists assume it’s false. This statement shows him to be either a liar or an idiot. Creation scientists make it very clear that they assume the Bible is true, but it is NOT true that scientists assume the bible is false. Rather, they don’t assume it’s true. Huge difference. Still, as usual, creationists just read this stupidity and pass it on as if it were itself the word of God.

NOTE: The service I was thinking of was not EBSCOHost, but SCOPUS.

New Video on Creationist Use of Probability

I've made a number of videos on the creationist misapplication of thermodynamics (maybe I should replace these with a single video that puts in all in one place). The central problem is that the creationists are using scientific principles they do not understand. I think I've said everything that needs to be said for the time.

I want to do a video now on probability. Hopefully I can say everything that needs to be said in one video. My sources will be essays by Ian Musgrave (at talkorigins.org), Murray Gell-Mann, Heisenberg, NKS, mathworld, and a few others. As with the thermo videos, it could be that this will turn into a series of videos. There's quite a bit of material.

Thermodynamics: Request for Criticism

So I read stuff - and I read really, really slowly - and I try to figure out what is being said and to the degree I'm capable of doing it, I try to explain it to other people. Unfortunately, I'm not actually an expert in the stuff I talk about. Of course, I'm not an expert in anything of consequence, but I'm particularly uninformed about certain topics that I blog and vlog about. As with most ignorant people, however, my ignorance is no deterrence to my opining on the subject. I take small comfort in the fact that most of the people debating creationism seem to be even more confused. Besides, Qui docet, discet. The more I try to figure it out and explain it, ideally the better I'll come to understand it.

So I'm trying to discuss the second law of thermodynamics (2LOT) and I'm reviewing and thinking about it. It's a non-trivial subject, of course, easy to be confused about.

I've tried to explain what I think I know a few times on youtube:
(Not necessary to view these to understand my point below)

"Using Scientific Definitions: Evolution and Thermodynamics"
"Abiogenesis does not violate the second law"
"Creationism vs Thermodynamics part 1"
"Creationism vs Thermodynamics part 2"


But there's something I'd like an opinion on - a fair opinion from someone who actually has a detailed understanding of the subject and not just someone with an opinion.

I want to explain thermodynamics in a way that people can really understand the issue and not just get confused about it. It would be better if a more knowledgeable person explained, but I think that sometimes the more knowledgeable people have explained things in metaphor - and have unintentionally murkified the subject.

Let me start by saying that some terms in science are not well-defined: or rather, there are multiple definitions that are not all equivalent.

There are numerous statements of 2LOT, but they are all equivalent (when you account for slight differences in vocabulary). But there are other words that are not so well-defined. There are several different definitions of randomness - and I'm pretty sure they're not all equivalent. In any given case, the definition is probably clear. Another word with multiple definitions is complexity: there are two definitions just in computer science which are not equivalent (namely computational complexity and algorithmic complexity). These are very different from what people mean when they talk about organizational complexity or about organic complexity (at least they are not clearly equivalent to the other two).

Finally, there is the word "order" that keeps cropping up as a common metaphor for 2nd law:
2nd law says that order decreases - life dies and decays is a clear example.

To me this is ONLY a metaphor. Order, I think, in 2LOT refers ONLY to thermodynamic order and not to any other kind of order. Thermodynamic order may have no relation at all to other kinds of order - biological order, various lay conceptions of order, etc.

Suppose we have three cases:

1. an elephant
2. a mass of protons (equal in mass to the elephant), but in the general shape of the statue of liberty
3. a mass of protons (equal in mass to the elephant, but in a sphere the size of a pea

Now we ask which of these 3 cases displays the most order - and we ask three different people: a biologist, an artist, and a thermodynamicist. I think it's very possible - and even likely - that these 3 different people could give 3 different RIGHT answers.

However, the 2LOT can only be applied using ONE of those answers. What I'm trying to point out is what I think is a less misleading analogy - one that is less metaphor.

1. Is my analogy above correct, slightly flawed, or completely wrong?

I think that people have come to misunderstand the metaphor as a reality. It's not even clear to me that some scientists make the distinction - which leads me to question my own understanding. Unlike the creationists who keep saying the same stupid thing over and over, I would genuinely like to be corrected, if I'm wrong. (Bear in mind I'm not going to believe I'm wrong just because someone tells me I'm wrong.)

In a recent and otherwise lucid and informative article at Scientific American, titled "A Simpler Origin of Life" , Robert Shapiro says:
"Life is distinguished by its great degree of organization, yet the second law of thermodynamics requires that the universe move in a direction in which disorder, or entropy, increases."

This sentence is in two parts, both of which I agree:
"Life is distinguished by its great degree of organization"
and
"yet the second law of thermodynamics requires that the universe move in a direction in which disorder, or entropy, increases."

What I think is misleading is the conjunction of these two phrases. The relation between thermodynamic order and biological order is not obvious. I would like to know what thermodynamicists think.

Note that I don't discount the importance of trying to explain the origins of complexity in nature. Surely this should be a primary concern of researchers in abiogenesis. My only problem is in conflating biological order with thermodynamic order.

Thermodynamic order, if I understand correctly, relates to only one thing: How much energy in the system is available for doing work. And I'm pretty sure that any other explanation is just wrong. I think we should avoid using words like "order" and "complexity" - not because they're wrong, but because they're too apt to be confused with the lay conceptions of those terms. I'm not saying the word "order" is wrong (particularly in statistical mechanics ... seems to make perfect sense there), but only that when it's used in explanations to lay people (like myself) that it's a term that is so laden with preconception that it's bound to be misunderstood.


2. Is Robert Shapiro's sentence misleading or is his implication clear and correct?

I thank anyone who responds in advance.

Nature's guide for mentors

There's a feature article in the 14 June Nature about the importance of good and early mentoring for the career of a young scientist, and the hallmarks of a good mentor. I'm the division coordinator for interns at work and I try to hook each intern up with a good mentor. Although not all of the interns are actual scientists, they are all doing research of some kind and I think the lessons of the article are largely directly transferable, including respect, encouragement, enthusiasm, being well-read, and picking the right kind of projects for them. Of particular interest was the idea that good mentors don't just mentor their designated mentees, but generally of people who are junior. A lot of companies could benefit from reading this article.

A problem in for-profits is it can often be a hard sell to invest time in junior people who might be destined to go on to bigger and better things - seeding the environment, as it were.