Registration is one solid solution, the other being the captcha. A captcha is an image containing numbers or letters which must be retyped in a corresponding entry field. Because it is an image and not text, bots typically cannot recognize the text and it usually foils their attempts to post comment spam (although it does not help against trackback spam).

It means more work for commenters but is definitely less intrusive than registration. Registration works too; it does have the benefit of creating a community of readers/commenters along with the disadvantage of disuading the casual commenter.

"More work for commenters" to type in a string of letters, maybe. But lots less work than erasing hundreds of emails.

Anything you need to do is fine with me.

I am in favor of Capcha if it works. I am in favor of requiring registration if it works (it can't be automated, though. People will just automate the registration process to spam).

One other alternative I have seen used is to take the Post button away and just leave the preview button. Then the user types his/her comment and clicks Preview. They see the preview and from there they can press Post.

I'm sure someone will figure out a way to make spam bots get around 'Forced Preview', but it might work for a while and is probably the least intrusive mode. (Plus it should help cut down on mispellings.)

What I am trying to do here (in this discussion) is to "teach science".

I do not mean "teach biochemistry" (although we seem to cover more and more of it) nor teach any any specific science but to "teach science" in the sense "teach what it is that scientiets do".

Most people get some history, some math and some literature in their education but they don't really learn what scientist do as an intellecutal activity.

As I said, Science is a way to reason that is not natural, that is usually misunderstood by people who don't do it for a career but which is unexcelled at the only thing it tries to do: learn what the universe is and how it works.

I have no intent to convincing people who don't believe in evolution that evolution happened (or that the universe is 12.5 billion years old or that quantum indeterminacy is real). I won't convince them because the reasons they have for not believing in science are theological or philosophical and science, a different way to approach things, has nothing really to say about their religion or philiosophy.

But it would be nice if those who struggle through all these posts at least see how the reasoning works.

Of what Q posted there his definition of "Scientific Method" and the difference between that and what a philosopher or mathematician does is the type of reasoning I am talking about.

In the main discussion people seem to think that science is only able to investigate things someone can do over and over ("if I heat ice to 2 degrees C does it melt") not something that happened in the past ("Was there ever a glacier covering Minneapolis? Say during the last Ice Age")

Science is a way to reason. Yes, you can use science to try to figure out if something happened in the past. Even to figure out something that can only happen once. The Big Bang can happen only once (per universe. By definition) but you still can use science to test if it did happen.

You could do this in lots of ways (every one join in). But you can't say "I see that there are lots of small lakes in Minnesota. And I will theorize that small lakes were scraped out by glaciers. Now I will look at Minnesota, see lots of small lakes, and say "See - proof there were glaciers!"

That reasoning is circular.

The reasoning I gave for the Alvarez theory about an asteroid killing the dinosaurs off was different. The Alvarez, pere et fils, said _if_ you looked in the rocks (no one had yet) you would find elements associated with asteroids (iridium) and _if_ you then looked at where the iridium was relative to the dinosaur fossils, all the dinosaur fossils would be _below_ the iridium.

So they made a prediction as to what people would find in the rocks. Had anyone found a bunch of dinosaur fossils above the irdium the Alvarez hypothesis would have been junked.

Everyone see the difference? One theory (the small lakes idea) uses the data you were already looking at when you saw the correlation, then looks again at the same data to see if the correlation was still there.

The other (the fossils relative to the level of iridium) predicts something no one had looked for yet and, indeed, predicted correctly what was found (and the Alvarez theory didn't _prove_ the asteroid killed the dinosaurs, but showed a way people could prove the asteroid did _not_ kill the dinosaurs.)

Drew,

I understand the difference. I had never thought of it before, but I understand it. But that is still not what I would consider science. The Alvarez theory sounds really great. But it doesn't hold nearly as much water as gravity. No one saw the asteroid when it hit. No one saw the dinosaurs. Not only that, but no one has ever seen an asteroid do what Alvarez claims it did at any other time either(to the best of my knowledge). There may be a ton of evidence to support the theory, but there is no empirical data.

What if I have a theory that says the dinosaurs were nuked by aliens and that the bomb left a layer of iridium over the fossils? I go out and find iridium above all the fossils, and bam, great new science, huh? Now we could easily disprove that theory by showing that aliens don't use nukes that leave iridium behind, or that aliens don't exist, or something equally absurd.

But that doesn't seem like science does it? Tell me what's different between that and what Alvarez did.

When I was in school my professor loved to talk about cold fusion and how it was a perfect example of bad science. But what happened afterward was a perfect example of good science. After those two guys, I forget their names, claimed to have discovered cold fusion everyone else went to their own labs and tried to recreate it. No one could. Theory debunked.

Now if these guys had said that they had conducted cold fusion thirty years prior, and that they couldn't recall the conditions of the experiment then we would all be relegated to dealing with their claims like we deal with Alvarez's. We could theorize and speculate all we wanted, but we could never disprove their claim unless we disproved something ridiculous, like say that atoms didn't exist.

But just because atoms really do exist doesn't mean that cold fusion does. Doesn't that make sense? Can't you acknowledge the difference between something like gravity and something like evolution?

To Luke mostly:

Luke said “What if I have a theory that says the dinosaurs were nuked by aliens and that the bomb left a layer of iridium over the fossils?”

Actually let me give you a better example. Because I might be able to point at some feature in that layer of rock you would find if an asteroid strike occurred but would not find if a nuclear weapon went off. Why not just postulate that aliens caused the asteroid strike? That they pushed an asteroid out of orbit and into the earth?

I wouldn’t postulate alien intervention because of Occam’s razor ("you don’t needlessly multiply extra agents to explain what happened"). The problem with the alien nuclear weapon idea is that you can explain _anything_ by postulating a sufficiently powerful intelligent being, rather than the natural results of the laws by which the universe operates all the time.

Your idea is “unfruitful”. Science doesn’t choose to needlessly multiply outside agents, and by sticking to its rules science “works” (it succeeds at figuring out the laws by which the universe works). The proof it works are the difference between the world in 1500 and the world in 2004.

Luke said “that is still not what I would consider science” and “there is no empirical data”

But that is what scientists consider science. I am unclear what you mean by “no empiric data.” The iridium, its location in the rock and the location of the fossils in the rock are data. And the little glass and fuzed quartz droplets are data. How does my reading of a thermometer to see what the temperature of the solution was after that chemical reaction occured differ from my looking in a rock to see whether the fossil is above or below the iridium? Both are looking at the universe to see if the universe did what I predicted it would do.

Hmm, is this what bothers you: In the thermometer case _I_ caused the chemical reaction. In the fossil case I didn't cause the event. (But in both cases I look to see if it occured).

There are lots of features of the universe that scientists look at without causing the feature to appear. Stars (no human ever made one), lava flows, continental drift.

And your favorite, gravity. We didn't actually make gravity. We are just observing its activities "in the wild" as it were.

Re cold fusion:

Yes, sometimes science gets things wrong. More often it gets things inaccurate/incomplete. But science continues to measure itself against something (the universe or more accurately the things we measure/test/observe in the universe) and slowly makes progress learning about the universe. There is often a Two-Steps-Forward-One-Step-Back dance (the development of our knowledge of the structure of the atom had a lot of wrong ideas. For example for a while they thought electrons were _inside_ the atom and the nucleus (well, what they thought of as what we think of as the nucleus) was the whole shebang. Then they found the nucleus only occupied a small volume relative to the volume of the atom as a whole. Quelle Surprise!.

But progress was made and our knowledge of the structure of the atom has advanced.

Luke Said “Can't you acknowledge the difference between something like gravity and something like evolution?”

Tell me a difference. Both are ideas/hypotheses/theories. Both have data that support them. Both have been revised/fine tuned over the years as we have gathered more data.

You might say “Gravity is physical science, evolution is life science” but actually both are just the working of the few natural laws in practice (There are, so far as we know, only 5 really basic forces in the universe. The motion of galaxies and the mutation of DNA bases both are the results of those same forces).

No, I don’t see a difference in the sort of reasoning one uses as a physicist or a biologist. They use the same thought processes (with data about different objects).

Why do you believe gravity affects the motion of planets and galaxies?

To Luke, and to the other people who agree with Luke but aren’t being as thoughtful and verbal in expressing their opinions (hint hint-start chiming in people).

I gather you do believe in gravity.

There are 5 basic forces in this universe, at the present stage of development of this universe. (The forces have "changed phase" (mutate) over the history of this universe and might mutate again. But don't worry. If they do you will be dead (and matter as you know it will no longer exist) at the speed of light. They changed repeatedly during the first few minutes after the big bang but haven't changed "recently" (last 12.5 billion years). Those forces are in order from top to bottom:

Dark Vacuum Energy
Gravity
Electromagnetism
Strong Nuclear Force
Weak Nuclear Force

Not all of those operate at all scales of size/distance.

The Strong and Weak Nuclear forces operate only over very short distances (ie inside the nucleus of an atom). They do not have any effect on what happens over larger distances. For purposes of that last sentence the diameter of a water molecule from side to side is a “large distance”.

Gravity and Electromagnetism operate over medium sized distances and on medium sized objects. The reason they are familiar to you is that you are a medium sized object. So is the sun for purpose of this paragraph.

The Dark Vacuum Energy operates only over very vast distances. “Very Vast” means that over “small” distances like the diameter of this galaxy you can’t detect it having any effect.

I bring all that up to point out that showing a force explains a phenomenon/observation at one scale does not necessarily mean the force explains a phenomenon/observation at very different distance/size scale.

So Luke goes into the lab and makes a long vertical glass cylinder, makes a vacuum in the cylinder, drops a steel ball bearing inside the cylinder and measures how if falls and convinces himself by repeated experiments that “gravity” is a valid hypothesis. He might even then go up to the international space station and test two 10 kg lead balls and measure very accurately the attractive force between them at varying distances.

Then Luke looks at:

Jupiter orbiting the sun
A binary star pair orbiting each other at a distance of 3 Light Years
Two galaxies orbiting each other at a distance of 3 million light years.

And you conclude (I am assuming you conclude, tell me if I am wrong) that gravity is the reason those are orbiting at the speed and distance you observe.

Why do you conclude that? You will have (being careful) predicted from your measurements in the lab how the motion of Jupiter, the binary stars and the two galaxies should move based on your theory and calculating for those much larger distances and masses. But you will also have observed the motion of Jupiter, the binary star pair and the two galaxies to make sure the theory still is holding.

You have never actually made two galaxies and (repeatedly) put them near each other, given them a little shove, and seen how they move in an experiment you constructed yourself from top to bottom. You are observing things that were already happening before you started the experiment to make sure the hypothesis about gravity still holds at that scale of mass and distance.

And if you go to extremely huge distances (billions of light years) or extremely tiny distances (inside the nucleus of an atom of oxygen) you will find matter following very different rules.

So I think (if you reflect on it a bit) you will see your acceptance of gravity is based in part on observations of the universe as you find it, not just on specific configurations of the universe you set up in the lab.

Drew stated I don’t see a difference in the sort of reasoning one uses as a physicist or a biologist. They use the same thought processes (with data about different objects).

I know you don't see a difference. But, in yet another rare glimpse of Left Wing Drew, that is because you have a higher opinion of human nature than I. I work with "hard" scientists on a weekly basis and other social scientists on a daily basis. I rank the theories of human behavior as much less probable than the theory of gravity, but as much more probable than theories that represent what Luke dubbed "scientific history". I see how scientists think. However, I am loathe to just use personal examples, which is why I recommended you read Kuhn. Kuhn spent his career studying scientists and the history of science. Kuhn's main finding, with which my personal experience strongly supports, was that scientists rarely allow a discover (or many discoveries) to falsify their pet theories. They will keep changing it, or dismissing other evidence as irrelevant or non-scientific until the day they die. It is the younger scientists who have no attachments to the old theories who study the new theories.

Let me give you a personal example. In one of your comments to Lucy, you stated. Tell me some test, something you and I can both observe that will be "A" if the earth is 1 million years old but "B" if the earth is 4 billion years old. If you can come up with that test, and if we all observe A then the Old Earth theory goes the way of the heliocentric universe and your view is the new working hypothesis.

According to both Kuhn and my own observations about human nature, this is wistful thinking. Such behavior depends upon human beings acting in a logical, reasonable, and selfless manner. It rarely happens. The minute someone points out some tests (or discovers some data that disagrees with the original theory), human nature will assert itself. The champions of the old guard will either dismiss the evidence ("their methodology was sloppy" or "that's not science even if they did follow the scientific method"), state their theory has some holes in it, but it is still the best theory around so we'll keep it until something better comes up (while marshalling all their forces to attack any theories that may start rivaling it), or simply say that upon further review, the new evidence actually makes their old theory stronger, the old theory just needed some revising. This latter tactic, known to politicians as the "big lie", is only used when it is impossible to dismiss the new evidence.

Gould is a textbook case of this last category. Gould's theory of punctured equilibrium was completely data-driven. Darwin's theory predicted a slow change. The fossil record did not support this. This evidence could no longer be ignored, biologists had been doing so for over a century and their claims that eventually someone would find evidence were looking weaker every decade. Knowing the data in advance, Gould came up with the punctured equilibrium theory. This is a prime example of human nature, and scientists are just as human as everyone else.

Let's try another example. I know you are unfamiliar with many of the newer scientific theories (as judged by your stated unawareness of terms and theories that have become more prevalent over the last two decades). Early next week (hopefully Monday), I'll start the next post on our larger thread, one about the age of the earth and the universe. I'll anticipate the results and predict that we'll be able to come up with scientific arguments that should falsify both the old earth and new earth theories. Human nature being human nature, it will not. Both sides will go on thinking they are being scientific and that members debating the other side are allowing their own biases to cloud their thinking.

This is why I agree with Luke about some fields being much more reliable than others. The more easily a theory can be tested, the less room there is for human rationalization and subjectivity. The more difficult it is to test (and disprove) a theory, the less reliable the theory because of both the difficulties in testing and because of human nature.

Drew,

Forgive me for not being as clear as I should have. As far as Alvarez's experiment, it was a great example of what I would consider science. Make a hypothesis and test it. And then let everyone else test it. The issue I have with Alvarez, as I understand him from your postings, is that he then concluded that the asteroid killed the dinosaurs. If his hypothesis was that iridium would be on top of all the dinosaur fossils, then that is a reasonable hypothesis which can be tested. If his hypothesis was that the asteroid killed off the dinosaurs, then finding iridium above their bones is not sufficient evidence to support that claim. I think you said yourself that some noted scientists think that the dinosaurs were already dead by that point.

That is the point I am trying to make. Just becuase there is iridium above the bones doesn't mean that the asteroid killed them. There is no way to observe the dinosaurs dying. Contrast that with gravity. Like you said, I can observe it with my own eyes, or my own instrumentation. It doesn't have anything to do with whether or not I caused the phenomenon I am observing, only that I can observe it. Who observed the dinosaurs dying? Who observed evolution? Who observed gravity? Me and you and everyone else. That is the difference.

I think what you are defending is what they would call circumstantial evidence on Law and Order. I don't watch Law and Order and I'm not an attorney, so correct me if I'm wrong. That would be in contrast to whatever the name for that is, I'll call it hard evidence.

For instance, lots of people think that Lee Harvey Oswald killed JFK. No one saw him do it. But there is plenty of circumstantial evidence to suggest that he did: he had a rifle, he was in a position to do it, he shot a cop right afterward. But there are still many people who think that it was someone else. Why? Because no one observed it. Contrast that with Jack Ruby killing Oswald. No one doubts that he did it. That's because we've all seen the video, hard evidence. There is no doubt, or at least very little doubt. Oswald killing JFK is like evolution. There may be evidence, but it is nowhere near as compelling as the evidence for Ruby killing Oswald, or gravity.

It doesn't have anything to do with biologists or physicists. Good science would be like a biologist hypothesizing that kangaroos have pouches. He finds a kangaroo, and observes a pouch. I want to verify this and I go and observe a kangaroo too and voila, hard evidence, good science. C'est magnifique, non? On the contrary, a physicist could hypothesize that the universe was created via a big bang. I want to verify this so I, what? Look at some circumstantial evidence, something that suggests a big bang but is not an actual observation of it. It may be very convincing, I may have to be well educated to understand it, but it is still mediocre science.

You are undoubtedly better educated than I am, and probably smarter too. But please don't keep introducing all these above our head discoveries and hypotheses. It is not necessary, and it only obfuscates the question. That is why it is so hard to ever address this issue because everyone gets lost in the jargon.

I've never seen a better explanation of why fisticuffs is called the "sweet science".

On the other hand, I just happened upon the assertion, sorting magazines a couple of hours ago, that Jack Ruby actually killed a man named Alek James Hidell, and that Oswald is in a secure hiding place. Oddly, every expose of The Truth about the Kennedy assasination offers a different selection of evidence, and comes to a different conclusion.

And by the way, Occam's razor is not science, that's philosophy. You can't say "This Universe actually does not care if you find evolution hard to believe. Evolution happens to be how this particular universe works, however, which is the only question on the table. This Universe also does not care if you find quantum indeterminancy hard to believe (evolution is nothing compared to quantum indeterminancy). Me, I would not have chosen quantum mechanics as the basic (probably only) building block on which to construct a universe. But I wasn't asked," and then discard theories because they are hard, or harder, to believe.

The First Time I Went to England

That last post by Q reminded me of something. The first time I went to England (I am from the United States).

The first time I went to England I had lots of problems. I assumed I spoke the same language as the Brits. Tread lightly here. I say "science" and he says "data-driven" and we don't have any idea what the other guy is talking about.

As usual my overheated brain sees 12 or 15 different things to say. I will try not to say all of them at once.

1) Q mentioned Social Scientists. I don’t know anything about Social Scientists. I think everyone who has struggled through all 32K of this thread understands what I mean by “reasoning using the scientific method (hypothesis/test hypothesis/revise hypothesis/test revise hypothesis). Do Social Scientists do that? I haven’t a clue. I gather there are different sorts of social scientists (sociology, anthropology, uh, other stuff) and they may not all do the same thing with their minds.

I do know the word “Science” on the door of the department has nothing to do with that. Political Science doesn’t use scientific method. It is that other, older, broader definition of “science” Q gave: knowledge. Computer Science doesn’t use scientific method. It is a first cousin of philosophy and mathematics and sort of a distillation of logic. Science it is not.

Psychology I know a little about (my daughter in law is about to get her PhD in psychology and we discuss it a little. And I know a little about it from my own training. It does try to sort out human behaviour and “the mind” (different from “the brain” that a biologist studies). Psychology strikes me as a science in its first, early stages before it has really sorted things out. Psychologists do try to use the hypothesis/test algorithm but they are (as an analogy to physics) not at the level Einstein understood gravity and not at the level Newton understood gravity but maybe at the level Galileo understood gravity. (I am being kind. I have a daughter-in-law in the field). This isn’t a failing on their part. One has to start somewhere (physics is about 350 years ahead of them) and “gravity” is probably easier to map out than “the mind”

Re Kuhn (and Lucy) and do scientists really change their minds:

Do you know about the Dark Vacuum Energy? Physicists didn’t either in 2002. Now they do. New data. They changed their position (on a dime). (Dark Vacuum Energy is basically anti-gravity. It is a force that _repels_ two masses whereas gravity attracts them. Actually (like gravity) it is a property of space-time, not of mass. But we found it this calendar year, as I recall, so there it is. Now everyone has to deal with it.

The “champions of the old guard” will try to refute the Young Turks data. (Take the “Dinosaurs are warm blooded” squabble.) Good. They should. You can’t just waltz in here and tell me dinosaurs were warm blooded. I will fight you every inch of the way, be really critical and make you actually prove it.

But then we will agree and move on.

There aren’t a lot of physicists left that believe in Newtonian, as opposed to Einsteinian mechanics anymore. Yes, some of the old curmudgeons had to die, but that conservativism serves a purpose. You need to be flexible, but not too flexible.

But Science (different from philosophy or religion or lots of other ways to reason) does have an ultimate arbiter: What really happens in the real universe.

Lastly (re Q) on “data driven”:
He tells me this is “one of the newer scientific theories” and I still have never heard of it. I am pretty current in physics, astrophysics, biology, biochemistry and paleontology. Never heard of it.

I am trying to think of an area of science that _isn’t_ data driven.

Newton didn’t hypothesize his view of gravity from first principles (like mathematicians do) then see if it held up. He already knew and was trying to explain the motion of planets and the motion of bodies (like a brick) near the earth. Einstein didn’t hypothesize General Relativity. He used a branch of mathematics somebody else had thought up previously (tensor calculus) and saw that gave a nice explanation to a perplexing observation (that the apparent speed of light is the same for you and I even if I am traveling parallel to the beam of light at 90% light speed) but he didn’t just muse on General Relativity, he was trying to explain a troubling observation (data).

(Newton, by the way, did the opposite. Newton invented a new area of math - calculus - to explain the observation. Einstein applied an already developed, but little used area of math).

I guess the Alvarez theory is sort of hypothetical. But that was based on data too (what causes 98% of all the species on earth to suddenly vanish at irregular intervals every few hundred million years?)

I await Monday’s post from Q.

Meantime I want to do some scientific reasoning here with the audience (to be continued)

There are some other qualities of scientists, if you are interested.

a) they assume things can be understood. Not all kinds of reasoning make that assumption. I am Catholic. Catholics believe there are things (what God is like “internally” when not dealing with our universe) that are completely beyond human understanding. (I agree). But regarding this universe I assume I can understand it because to do otherwise is “not frutitful”.

b) scientists, when stumped by a large problem they cannot see how to solve, turn instead to a smaller problem they do think they can solve. They assume that by solving a lot of small problems they will eventually make progress and see how to solve the big problem.

So I want to discuss why it is that Luke (and maybe Q and maybe others) see some marked division in kinds of science or data or experiments I don’t see.

I would ask you all to _not_ deal with evolution nor with biology for the moment. I am trying to isolate what the gap between my understanding and yours is, and I suspect it may be “living stuff” vs “inanimate stuff” but first I want to work out some questions about what an experiment is and historic data.

I suspect (other than the belief that animate matter has one set of rules, inanimate matter another set of rules) there is either a difference between me and Luke regarding

a) the kind of data one gets if one sets up an experiment in the lab and the kind one gets if one observes nature “in the wild”.

b) the kind of data one gets from looking at what _did_ happen in this universe in the past vs the kind one gets by doing a prospective experiment.

Does Luke, Q or anyone else see either of those as the problem?

There are experiments one sets up in the lab (“in vitro” literally “in glass, in the test tube as it were) and observes in nature as one finds it (“in vivo” literally “in life”).

There are a couple of reasons scientists gather data “in the wild”.

1) There are data one just can’t get in the lab. The thing you want to measure is too big, too hot, too dangerous for example. You may not be able to see the effect with something smaller than a galaxy (a galaxy isn’t large enough to detect the Dark Vacuum Energy. You need to look at about 3/4 of the visible universe to see it).

You could, in theory, study supernovae by making them and setting them off. To survive the experiment you want to set it off some distance from you (another galaxy is about the right distance. Say 1 million light years). Now that _is_ possible (make a huge star, set it up that it will go supernova when you push a button (the button dumps a lot more hydrogen into the star), push the button and look in your spectrophotometer.

Since you want to be 1 million light years away, it will take 1 million years for the signal from your button to set off the supernova. And another 1 million years for the light to get to your spectrophotometer. 2 million years all told (much shorter and you are dead, not published). Do you have any idea how long it will take you to get tenure if each experiment takes 2 million years?

But that _is_ possible.

There are experiments that just are not possible (if you and the universe intend to be around to see the answer).

Remember I mentioned that this universe has changed phase (changed its physical laws) a few times. That was in the first second (millisecond). What was the universe like then, when gravity, electromagnetism, and the strong and weak forces were just one force?

That happened when the energy (uh, temperature) of the universe was really high. So you could try to duplicate that in a supercollider. If you _should_ succeed in achieving sufficient energy something bad will happen (in the physicist sense of “bad” These guys regard thermonuclear bombs and supernovae as “interesting”). The universe will have a phase change. It will extend in all directions at the speed of light. Behind the wave-front of that phase change a) people will be dead b) atoms won’t exist c) even electrons, neutrons and protons won’t exist (the rules of physics will be wrong). Basically you will destroy this entire universe.

Physicists are building a really powerful collider (“cyclotron”) at CERN. It is so large it is part in France and part in Switzerland. It is intended to make energies closer to the Big Bang than what we currently can make, so we can learn more about the Big Bang.

Being sane, the physicists first calculated the energies to make sure they wouldn’t be so large as to cause a phase change. Because otherwise when they pushed the on button the universe as we know it would disappear.

But CERN is safe and under construction. They will likely do the math again before building the next generation after that.

(Sidebar on parnoia:
There are billions of stars on the surface of a sphere with a radius of 100 million light years from earth. If, anywhere on the surface of that sphere, any physicist built a collider that is too powerful and didn’t do the math first, and he turned it on 100 million year, 5 minutes ago the universe is toast. And the wave front will be here in 5 minutes, to tear your subatomic particles to pieces. But you can’t see it coming because it is coming towards you at lightspeed.

Have a nice day)

So you _cannot_ test in the lab the energies of the first microsecond of the universe (and have the universe survive).

So physicists look at “fossils” (their term): Things left over from that microsecond. Strange particles that are still flying around. The large scale structure (how the galaxies and voids between galaxies are distributed), the cosmic background microwave radiation (the left over heat) and the smoothness of distribution of that heat in space.

Those are the only data they can collect.

2) In Vivo vs In Vitro.

Remember what I said about the genesis of elements (Hydrogen to Oxygen to Iron). We know that _can_ happen in the lab. But is that how is _did_ happen in the evolution of the universe?

Biologists spend a lot of time worrying about this. Just because you can break this carbohydrate down into that sugar by this specific chemical reaction in a test tube doesn’t mean that a red blood cell in your spleen uses that particular reaction instead of some other reaction.

So you need to look in the real live sauvage universe to see if it does in the wild what you can do in the test tube.

Those are two reasons scientists collect data in ways other than laboratory bench experiments.

(Going way back)

Does the collection of historic data or the collection of data “from the wild” bother anyone that such data invalidate the scientific method?

Q said "Gould's theory of punctured equilibrium was completely data-driven. Darwin's theory predicted a slow change. The fossil record did not support this."

No. There is slow change. All the time. That explains those beaks on the finches in the Galapagos. And the small horse to medium horse to large horse (losing toes gradually in the process).

Gould is talking about the mega changes when 98% of all species vanish in the blink of an eye. After those happen (in a world full of opportunity and with no competition anymore for "large plains grazer" or "shoreline scavenger" there is a burst to fill all those open niches from some unlikely survivor.

Luke stated:

It doesn't have anything to do with biologists or physicists. Good science would be like a biologist hypothesizing that kangaroos have pouches. He finds a kangaroo, and observes a pouch. I want to verify this and I go and observe a kangaroo too and voila, hard evidence, good science. C'est magnifique, non? On the contrary, a physicist could hypothesize that the universe was created via a big bang. I want to verify this so I, what? Look at some circumstantial evidence, something that suggests a big bang but is not an actual observation of it. It may be very convincing, I may have to be well educated to understand it, but it is still mediocre science.

Exactly. If something is not observable, testable, and repeatable, it is mediocre science at best. That is not to say we should not try to understand the past, but it is foolish to give any theories about origins science (another word for Luke's historical science) the same credence we give operational science.

Drew had a question about social scientists.

Q mentioned Social Scientists. I don’t know anything about Social Scientists. I think everyone who has struggled through all 32K of this thread understands what I mean by “reasoning using the scientific method (hypothesis/test hypothesis/revise hypothesis/test revise hypothesis). Do Social Scientists do that? I haven’t a clue. I gather there are different sorts of social scientists (sociology, anthropology, uh, other stuff) and they may not all do the same thing with their minds.

OK, another sidebar. We have a lot of those at our roundtable, especially on this megathread :-)

In academics, most scientists (social and otherwise) have very little background on the philosophy of science. It is not until a person pursues their doctorate that they actually spend more than a week on the subject. And even then, it depends upon the department and the school. Until I became interested in obtaining my Ph.D., I didn't realize that various schools have their own philosophies about how to research. It is important to this discussion because some schools strongly stress the scientific method (such as the research university I attended) and some do not. The two camps also argue quite a bit with each other. For example, those who do not give much emphasis to the scientific method argue that ever since Hume pointed out that the modern science depends upon two major assumptions (causality and induction) which are unproven articles of faith amongst scientists, science is no more accurate than other methods of research. These post-modern schools of thought depend more upon qualitative studies instead of quantitative studies. There are relatively few post-modern folk in the hard science community - at least those who admit it, I place many macro-evolutionists in this camp ;-) - but there are many amongst those who study societies and individuals. Those who use the scientific method to study societies and people are social scientists. I consider myself one of these. This is nothing new – social scientists have come up with many theories of human behavior and continually test them. Many end up on the ash heap of history, but others seem to work quite well (especially in the aggregate; it is much, much easier to predict how a mass of people will behave verses predicting the behavior of an individual).

This background is why I rank some "hard science" theories, such as the theory of gravity, as much higher than "social science" theories. However, both "hard science" and "social science" theories are operational science, they may be repeatedly observed and tested. This is why I give even social science theories much more validity than I give origins science (aka Luke's scientific history).

YAY! Posts not spam!

Re the Luke/Kangaroo/Pouch thing:

No. Dead wrong. Here is how it works:

I hypothesize a kangaroo has a pouch for some reason (no eggs and babies born too small to survive in the world (both of those are true).

You go find a kangaroo, test if the kangaroo has a pouch, find it does NOT have a pouch (we are talking female kangaroos here obviously).

You have _disproved_ my theory.

See the difference?

Re repeatable:

The experiment (a way to look at a kangaroo or a way to look at an early star for iron in the spectrum) is something that is repeatable in that any scientist (trained and with the right equipment) can also see the pouch.

If some other person can't also look at the star, or the kangaroo, _that_ is not reproducible.

More in a bit.

I want to do something "as an experiment" (Scientists think you can break a large, insoluble problem into small soluble problems. At least that is their operating assumption).

I want to talk (for the moment) not about life/evolution. I don't want to talk about the Big Bang.

I want to disect out the "can science tell what happened in the past" idea and deal with that thing I said about evolution of the elements (Hydrogen to Oxygen/Carbon/midweight elements then to Iron etc).

To recapitulate: This sequence is compatible with lab (cyclotron/accelerator) data and this is compatible with our general picture of the atom. But we would like to know (even if this is a possible way to get iron atoms) if this is actually the way this universe got its iron atoms. So we look for historic data too (in the spectra of old, middle aged (second generation) and new (third generation like the sun) stars to see which elements are in the spectra.

Those are repeatable experiments (anyone with a telescope (a big enough telescope) and a spectrophotometer can look at the spectral lines too). It is not "make a star, set off a supernova in the lab, look at the showere of elements" experiment though. And that (making your own supernova) wouldn't answer that question I asked about the history of this particular universe.

Do Luke, Quixote and others see that as "mediocre science" and if so, why?

I will get to the causality thing Q brought up eventually. It is a big subject because it has to do with time (how fast does it move and does it only go in one direction and does it go at the same speed for everyone) and probability.

There is a _lot_ of background before we can understand each other there.

I want to disect out the "experiment about what happened in the past" problem explained in my immediate prior post first (as if "immediately prior" has any meaning to the photons coming out of your computer screen . . . )

Hehehehe. So the plan is to send all the Democratic Senators out of the country?

"Why is he saying 'out of the country when the UN is headquartered in New York?"

Because there is a petition drive to get the UN headquarters thrown out of the US. I favor Darfur, but I would accept Port-au-Prince, Haiti as an alternative.

http://www.moveamericaforward.com/?Page=Petition

That would almost be better than chocolate! I don't care if he's a Republican or Democrat, but he IS Jewish. Personally, I think all our representatives to the UN should be Jewish. No, I'm not advocating this as a punishment to American Jews but rather a constant reminder to the UN that we find their anti-semitic policies appalling.

To Lucy:

Do you recall the days of Apartheid? The US sent a black ambassador to Union of South Africa [G]

That was a nice one too!

I'd be surprised if it were any other way. Afterall, soon there will be adults that never experienced life before the SciFi channel. Or the moon landing. Or Hallmark making StarTrek Christmas ornaments.

Well, I've been alive through most of the era of space exploration (I was born between the Zond 2 and Ranger 8 missions).

I've come to think of Darwin's theories as very useful for micro-evolutionary trend analysis but seriously flawed for macro-evolution.

When I was younger, I was disappointed in religion, because it didn't provide "all the answers."

As I get older, I'm coming to the conclusion that, maybe, science should try to provide answers and religion should provide questions.

I'm still a bit leery of any doctrine which requires "blind" faith, but whether divine intervention or extraterrestrial "seeding" is to blame, I'm more and more convinced that there is more out there than just us.

Of course, a far enough evolved civilization would be indistinguishable from the ancients' version of Gods in any event.

Basically, I just want to know who to blame! ;)

I think there's a fundamental flaw in attributing life on Earth to aliens. Where did the aliens come from? If abiogenesis is impossible on Earth, then why would you think it more likely on another planet?

Furthermore, one of the primary ideas of ID is that complex specified information (CSI) can only be produced by an existing intelligence. If you follow that proposal to its logical conclusion then the intelligence must have originally come from outside our known universe.

What is this "as more and more scientists abandon Darwin"? First I have heard of it.

Small sidebar on Darwinism: Darwinism is, like quantum mechanics and general relativity an idea that is pretty simple at its core, non-intuitive, talked about by a lot of people who are not talking about what the real theory says and profound, correct and changed massively our view of the universe.

The one "change" in Darwinism is that Darwin himself thought in terms of slow gradual change. That isn't right. We now know the change is occasional and fast ("punctuated equilibrium". You stay in one state for a long time, then suddenly (so fast the record in the rocks sees it as almost immediate) go to another equilibrium. That is an embellishment, not a refutation of what Darwin originally said, though.

Hmm, most people who talk about Darwinism are really talking about Lamarkism (Lamark said that the giraffes stretched their necks so their children had longer necks. Like saying that if you do a lot of weight lifting your children will be born with bigger muscles. Darwin actually said 1) the variability is random (no trend to longer or shorter neck). That was a huge intelectual breakthrough BTW. Before Darwin people defined a species (the red winged warbler for example) by a single platonic ideal in a museum collection. After Darwin people defined a species by collecting a lot of red-winged warblers to show what spread there was to the species. That is a very different view of the word "species"

2) It is the selection that is non-random (long neck lives long enough to have more kids). This is what Jacques Monod called "chance and necessity" which is a nice way to put it. Is that what you are talking about?

Species come to predominate by "compound interest".

K=K1*T^N. If one N is bigger than another N, the formula with the larger value for N gives a larger value for K as T becomes large.

None of this has anything to do with either God nor aliens. It is just arithmetic.

Many good comments on this thread. Here are a few more thoughts in response to some of them.

If abiogenesis is impossible on Earth, then why would you think it more likely on another planet?

I don't. I agree with your logic. However, Crick was a smart man and his theory was that while the evidence clearly refuted Darwinism (or macro-evolution) on earth, the theory was still viable. Thus it "must" have happened somewhere else in the universe.

What is this "as more and more scientists abandon Darwin"? First I have heard of it.

Ever read Kuhn? Must reading for any discussions about how scientists think. One of the things he pointed out was that most scientists rarely change their mind when a theory is being abandoned. A few key senior guys might, but in many cases none of the older scientists will move on to other theories. Instead, the younger guys – who may or may not be more flexible, but definitely have the advantages of being more motivated (they still have to earn their reputations) and having less baggage (they haven't spent a career refining the old theory) – spend time on new theories. The old theory doesn't go away until 1) the new theory is strong enough to better explain things and 2) the old farts die off.

Item 1 explains why Darwinism is still around – despite all the problems with the theory (which I'll briefly discuss later), it is the best naturalistic theory that biologists have been able to muster. According to Kuhn, a bad theory, no matter how flawed, will stick around in the absence of a better theory.

It is also difficult to falsify Darwinism since biologists keep it a moving target. As you mentioned, Darwin predicted change was very, very slow. The fossil record does not support this, so his theory was wrong. However, the biologists just changed the theory and created the idea of punctuated equilibrium to keep the idea of evolution alive in the face of what they were actually finding. Intelligent Design actually better fits the fossil record (in your words the rocks sees it as almost immediate) than supporting Darwinism.

However, the reason why I think (along with many other scientists) that Darwinism is on the way out is that the younger scientists (mostly molecular biologists such as http://search.barnesandnoble.com/booksearch/isbnInquiry.asp?userid=UH0kBpSAs9&isbn=0684834936&itm=1 ">Michael Behe) don't believe in Darwinism. Macro-evolution made theoretical sense when people thought cells were relatively simple and that a tiny tweak here or there could result in a fully functional new organ. If you want the details, buy his book (or one of the many like it, but Behe is a good writer). If you want a layman's view, I suggest Darwin on Trial by Philip Johnson. Philips is an attorney who shreds the claims of Darwinists in a clear and funny fashion. No matter what our beliefs about Darwin are, the main point is that I see more and more young scientists rejecting Darwinism. If this trend continues, as I predict, Darwinism will be on the ash heap of history when the older scientists die off.

BTW, a few years ago I was surprised to learn that Darwin plagiarized the idea of natural selection from Edward Blyth, a creationist. Now this fact somehow escaped all my biology texts…

Trying to deal with this in small bites:

"You are cheating because Darwinism is a moving target. And besides, it is just a theory."

Here is how science works. It is _not_ a way most people approach the world. But it is important to understand because it changed the world enormously (and still is) after about 40,000 years of trying to deal with the universe with a different set of intellectual tools.

Most people approach the world by "tradition" by which I mean "I did this before and it worked so I will keep doing it that way." As an example of tradition: Every time the tribe cooks a pig we all get sick. But if we sit around the fire and chant the names of all our ancestors, and all the hunts they were on (which takes about 2 hours) while the pig cooks, then none of us gets sick." That will work. Over and over. What is obviously happening is by doing all that chanting you are cooking the pig long enough so the microorganisms in the pig get killed. And you don't know why it worked, but you don't have to know why it works. It does and "tradition" in the sense of doing things you have done before with success is the second best way we have come up with to get along.

About 1500-1600 A.D. the western Europeans came up with a different way to do things. The ancients (the Greeks and Romans for example) were very bright and knew a lot, ie they were excellent at observing and reasoning. For example they knew the earth was a sphere and they knew the dimensions of the earth to within about 3%. But they didn't use science.

"Science" works like this. You come up with an idea of what will happen. Then you test the idea. The idea comes _before_ the testing. See how that differs from "tradition"? You do this by thinking up some action you can take that would turn out "A" if the theory is actually how things work but "B" if the theory is wrong. You do the test. If "B" occurs you scrap the theory and think of some other theory. If "A" occurs you are a bit more confident. Not certain (see below) but more confident. You then think up some other test ("C" if the theory is true, "D" if not) and test that. You keep doing this as long as none of the data conflict with the theory.

Some important points:

1) You _never_ prove a theory. You can't prove a theory. All you can do is _disprove_ a theory. Do you see why? If the theory does not fit one of the observations I have made, it is wrong. But if it fits every observation I have made that doesn't mean there is not some other observation I have not made which will show it wrong.

Let's take gravity. Newton came up with a theory of gravity. It was brilliant and it fit all the observations anyone made from the falling of an apple to the motion of the planets circling the sun. So everyone used Newton's theory. And it worked and they did all sorts of useful things they could not have done without knowing ahead of time where things would land when you tossed them into the air. They discovered planets for example. They could see the outer planets orbits were not following the predicted paths, they used the theory, it said "There must be another planet, further out, perturbing the orbit" and the theory told them where in the sky that further-out planet had to be, and they looked there very closely and lo! There it was (twice - that planet had one further out still, perturbing it).

But then the instruments got better and they found Newton's Law of Gravitation did not work perfectly. Mercury kept getting out of place. So they came up with a new theory, an embellishment/improvement built on Newtons (Eistein's law of gravitation which allows for warping space near the mass of the sun) and now they have a theory that is better.

Newton's theory is still good enough for most purposes. And people still use if for most purposes. It is simpler to calculate and the errors are tiny for anything you do on earth with normal sized objects. You have to deal with enormous velocities, masses and distances before you start to see the errors creep in. Then you switch to Einstein's theory.

Einstein's theory is not proven. We are still testing it. If we should find some odd condition (near absolute zero right close to the event horizon of a black hole? Who knows?) in which it does not hold, we will have to come up with a new theory to cover those circumstances.

Note that this "New Theory of Gravity" will have to cover all the old observations too. Einstein's theory covers all of the normal-speed normal-mass observations just fine.

2) The whole point of "science" is that it is predicitve. It tells you (ahead of time) what the observation will be when you run the experiment. Science, as opposed to tradition in the odd way I defined tradition above, lets you progress enormously faster in figuring out what will happen. Tradtition (in my sense of the word) keeps you safe standing where you are. Science lets you move out into unexplored areas of the swamp. That is why knowledge exploded starting in the 1600s. Science is the reason you have a cell phone, can feed 6 billion people on the world, didn't die of measles at age 2 years and live in a world where people can exchange ideas over the Internet.

3) You test against the universe. You don't just speculate. And the testing against the universe bit means there is an arbiter (the universe) making sure "your science" and "everybody else's science" is "the right science.

In religion or philosophy you can have one idea and I can have another. You can say you find inner peace while saying "Om" in the lotus position and there is nothing I can say or think or do to contradict that. If that gives you inner peace, fine. That is your inner peace. In science if you say "I think gravity makes things fall up, not down" we have a way to tell if you are right and all the rest of us are wrong. We will come to an agreement because there is a way to test. Note that you (who think before the experiment that apples fall up) will not only agree with me, after the experiment. You will agree with the universe too. That's important. Your cell phone actually works, it isn't just a philosophical cell phone that gives you an inner sense of connectedness with other people who carry the cell-phone talisman with them.

Science is good at telling you whether A or B will happen in the real, physical universe if event X occurs. Nothing else is anywhere close to telling us that. If you want evidence for that, look at the rate of accretion of knowledge of the universe before 1600 and after 1600.

Science does nothing _other_ than tell us what will occur in the physical universe if event X occurs. You can say "My eastern philosophy is superior to science because it enlightens me regarding the oneness of beingness" and all I can say is "that isn't what it is trying to do". You can say "But I choose to believe that the apple falls up and who are you to say I am wrong' and my answer is "The apple doesn't fall up."

Now on to what Darwin's Theory says and what Punctuated Equilibrium says (think of Newtonian and Einsteinian laws of motion) in a future post.

OK, Two more things. (I keep needing to set more background before getting to the "More and more young biologists reject Darwinism" statement”

Solipsism, Berkleyism, Christian Science and the Pranskter God:

I don't believe in any of them. Solipsism is a philosophical idea which says that the only thing in existence is my own mind. Even _your_ mind doesn't exist, let alone the physical universe. You can't disprove Solipsism. Berkeleyism (named after the philosopher, not the city in California. The California city is actually named after the philosopher) is similar. Christian Science (as I understand it) says that all our souls exist but there is no physical universe. That is why they don't believe in medical care. One of my college roomates was a Christian Scientist. (He was also a linemen on our NCAA college football team which is relevant to the following story.) I would ask him over dinner (this is a true story):

"So what if you got gangrene in one leg and frostbite in the other and both legs fell off and you couldn't walk. Would you admit then you hadn't any legs?”

"No. All that would prove is that, because I am not a perfect enough Christian Scientist I thought I didn't have legs and wasn't walking.”

"So what if I take this thing that seems to me, a non-Christian Scientist, to be a fork and stick it into the back of that thing that seems to be your hand?”

"I would seem (because you are not a perfect Christian Scientist) to break your arm. But your arm would really be broken, even though it would seem to hurt.”

That (real) conversation pretty much sums up my view of the "inner truth/no objective universe" crowd. It is impossible to prove the universe is out there, because they can always say "I am choosing not to look." But actually they do believe it exists. You will note the Eastern Philosophy crowd actually do come in out of what seems to be rain.

The "God the Prankster" people are a little similar. If I say "The sun is 4 billion years old and the evidence is a) the rate of fusing hydrogen to helium and b) the amount of helium in the sun are the amount it would take 4 billion years to make (I know, there is the background H2 from the Big Bang but you get the idea). They answer: "God made the sun 4004 years ago (or at 10 AM this morning) and he put that amount of helium in the sun to test our faith.”

With that sort of reasoning too we are not going to have any meeting of minds. Anything observed in the universe doesn't refute belief for the first crowd (the Berkeleyians) because they claim I am not really observing anything and doesn't refute anything for the second crowd (God the Prankster people) because they say "God made it just like that.”

For me there is an actual universe out there, external to my mind. And I assume it operates under non-capricious rules for two reasons:

a) If it doesn't, there is no point in thinking about anything

b) And my cell phone works. I.e. the point of view that there is a universe and you can predict some things about it (the quantum mechanics of the chips in your cell phone for example) actually get you someplace.

There are those who don't accept "get you some place" as having any meaning. The inner-peace Eastern philosophy crowd for example (see my last post). I am not one of them.

When he says "Darwinism" I get the impression the Admiral is not talking about Evolution (see my post on Darwin which is coming, honest) but may be talking about the divide between inorganic matter (a mix of Methane and Ethane gas) and living matter (a bacteria).

I would caution the Admiral that using religious reasoning to answer a science question is dangerous.

For example "can a mix of chemicals similar to those in the cometary halo make DNA in the laboratory" or "Can naked DNA molecules come to have a lipid bilayer isolating them from the surrounding chemical soup" (actually the sequence was probably lipid bilayer first then surface reactions and reactions in the pocket isolated by the bilayer for reasons of concentrating and isolating the right chemicals but that is a side issue). That is a science question. If you say "No, because God has revealed to me it can't happen" you are at risk of finding out actually it does happen.

That happened for "the earth is the center of the universe", the sun is the center of the universe" and, uh, Darwinian evolution.

Another question is "What about the soul?" That is a religious question.

Darwin discusses evolution of species including man. He doesn't say anything abou the soul. Drawing conclusions about religious matters based on scientific evidence is as likely to put egg on your face as drawing conclusions about scientific matters from religious beliefs.

As an aside, and the Admiral and I have discussed this before, I don't have any expectation that "the soul" is uniquely human. We may find other species on other planets that seem to have civilizations, relgions and moral codes. There are even some other species on earth that may have "religions" (I think).

Neanderthals are not our species. We did not evolve from them. They are not our ancestors (as far as recent data shows). They and we are cousins, but we are not their descendants. Neanderthals had ceremonial burial (flowers and hunting trophies and animal heads in the grave.). Sounds to me like they were pretty smart, and may well have done those burials because they were concerned about an after life. Did Neanderthals have souls? Who knows?

Koko (the gorilla) is sophisticated enough to know she has an emotional state and that her emotional state will possibly be different in the future. She was grieving (her pet died) and she said with her sign language she was "not ready to stop grieving yet" (the "yet" is the boggling word she used. If gorillas mourn the dead and know their emotional state from an outtside viewpoit do gorillas have souls? Who knows.

But I do know you can't answer the Neanderthal soul question with science. Nor the Life from Inaminate matter question with religion. Every time somebody tries that, they wind up looking silly.

Now maybe I can discuss Darwin.

Evolution according to Darwin

As I said, Jacques Monod’s description “L’hasard (random unpredictable chance occurrence) et la necessite (the inevitable sequela of that chance event) is a pretty good description.

1) Random event.

In olden days people thought of species as a single ideal. The Platonic Ideal Fox for example. A species is a collection of individuals who can breed with each other. There is a range that includes “horse” (Apaloosa, Arabian, Morgan). There are things that are not horse (cow) and things that are close (zebra, burro). “Burro” is right at the edge of being a different species from “horse”. A burrow and a horse can breed and have offspring (a mule or a jenny depending on whether the horse is the daddy or the mommy). But that offspring is almost always sterile.

But two horses have offspring that differ a little. Randomly. This one has slightly longer legs and that one slightly shorter.

There is no trend to this point. No push for taller horses. Just random wobble around a mean.

2) The Sequela

However of those offspring one (the tallest maybe) will have an edge in living long enough to have progeny. It has longer legs and runs faster. The difference is only slight but it is, say, 1% more likely to reach reproductive age than the horses that were shorter.

This “taller” thing is a random event parent to child, but NOT a random event child to grandchild. What I mean is that (we now know the molecular mechanism. Darwin didn’t) the parents randomly shake the dice cup and give “A” or “B” of each of their #11 chromosomes to the progeny. That progeny now has the B version of the #11 chromosome from the daddy and the A version of the #6 chromosome. And the A chromosome the daddy gives may not happen to be exactly the same as the A chromosome in the rest of the daddy.

(Sidebar: For example, in Queen Victoria there was a mutation in one of her chromosomes. She (but none of her forebearers) had the hemophilia gene. See below).

This mix of chromosomes the new taller horse has result in a taller mix of that horse’s progeny (thereafter). Actually they result in a mix for the grand-child horses too, but that random mix is now around a slightly higher mean.

(Sidebar: Once Vickie had that mutation it was also in her offspring down through the crowned heads of Europe. Until Lenin shot them but that is not the point here).

So there is a random spread, but not all of that spread are equally represented in subsequent generations.

Gradually (actually over surprisingly few generations) the “horse” changes and after a while the “horse” is lots taller than it was, even a million years before.

That’s basically the Darwin theory. Darwin thought this was going on all the time. It is. Darwin thought that was why there were horses, almost horses (burros) and not horses anymore (zebras). It is.

He missed one important detail of what shaped the world, though. Everything wasn’t always all that slow and gradual.

See next post.

Evolution according to Gould

You probably think Stephen Jay Gould is some guy who wrote books and a magazine column. Actually he is a pretty important figure in our understanding of why the world is the way it is. His idea is “punctuated equilibrium” and here is how it works.

There were all these dinosaurs. There were graze-on-the-plains dinosaurs and there were hunt-the-grazers dinosaurs. And they were all happy grazing and slowly evolving better teeth and longer necks and all that.

They were _not_ gradually replaced by mammals (who likewise eventually radiated into large plains grazers (horses) and things that ate plains grazers (big cats).

There was a Great Dying (a mega catastrophe during which almost everything on earth died.) For the dinosaurs that was an asteroid strike that changed the climate. Other things can cause a massive change, though. The change in the poles (they are “unusual” at the moment in that, in a planet whose surface is mostly water one pole is over land and the other pole in a shallow landlocked sea so we have polar ice caps and ice ages. That is rare for the history of the earth long term. It has happened several times, but usually it is much warmer). Almost every organism on earth died. Most species were wiped out completely because the living conditions changes so much the traits you all had evolved no longer were much use.

Randomly some other trait, never selected for in the past because in the past there were not ice caps or dust in the stratosphere or whatever the new situation is, were all that mattered and some unlikely critters (mammals in the current case) suddenly found all the competition was gone.

So the mammals, seeing all those wonderful job openings (Large Plains Grazer and Large Plains Grazer Eater) filled in the open positions.

Some things to remember:

1) Evolution goes on all the time. That is why you have organisms (“superbugs” in hospitals) that are resistant to all known antibiotics for example. This really truly happens and is going on around you all the time. Most of it (like continental drift) happens so slowly that short-lived humans have trouble measuring it. Some of it (the evolution of Methicillin resistant Staphloccoccus Aureus) happens fast enough to witness because the generation time of Staph Aureus is only about an hour. But it is always going on.

The bugs have a random resistance to Penicillin (or whatever). Those with more resistance have daughter-bugs. Those that don't, die. In a bit, the only daughter-bugs left are ones that can survive in the Penicillin-filled world we all now live in.

2) The Big Changes are episodic and catastrophic. There have been a number of them. The Dinosaur Killer asteroid wasn’t even the biggest. Those huge depopulations are what really shape the world, by opening up all those “opportunities” for the few survivors.

3) There is NO trend in any of this. There is no “steady progress” and no “higher organisms appearing.” There is no reason to say a stegosaurus is a “lower” plains grazer than a rhinoceros. There is no reason to say a velociraptor is “lower” predator than a lion.

Everybody (almost) dies. Some random trait that was of no use until that asteroid put 1/3 of the mass of the oceans into the atmosphere as steam suddenly becomes the only criterion for lasting out the next hundred years. Whoever is left can now become an efficient plains grazer because all that grass is there and nobody is eating it.

4) This is real. As real as the quantum effect that makes the chip in your computer work that lets you see these words on your monitor.

As real as the drug resistant bacteria that is killing somebody in the hospital down the street. That micooganism really did evolve to be resistant to methicillin. It wasn’t there 20 years ago and now it is. If you don’t believe me ask that person infected with the bug tomorrow. When they are dead.

Now we finally have enough ground-work laid that I can ask the question I have been wanting to ask.

Remember I said that Science (in the way I defined it) has the important attribute that Science predicts what the universe is going to do if you do “X”.

Let’s deal with a specific practical problem. Not with Evolution as Just a Theory but with whether we want to use that theory to help us choose our course of action.

For the purposes of this problem I am going to assume:

a) We all agree that bacteria exist.

b) We all agree some bacteria are resistant to antibiotics.

(if anyone doesn't believe both a and b raise your hand)

c) Some of us think that evolution is why these bacteria are resistant to antibiotics. (To rehash the last post, some of the daughter-bugs a while ago, randomly, were a little more resistant. By multiplying in an environment where the antibiotic was around those few, mutant bugs became the predominant strain and then from those semi-resistant bugs some of their daughters were even more resistant until we wound up with SuperBug that can grow in the presence of any concentration of any known antibiotic (or at least in the presence of any concentration that won’t kill the human host faster than it kills SuperBug).

d) Some of us (the ones who don’t accept Darwin’s theory) think God created some bacteria to be resistant to antibiotics. Just as he created all the other differences we observe between all the other species (Another side note: If you think that, you have to also think God is doing that all the time. He didn’t create all these species way back when, but is continuing to create new species. For example I can take a vial of bacteria that have NO bugs in there that are resistant to penicillin and do that grow-in-presence-of-low-dose-penicillin experiment described under “c” and the penicillin resistant bugs that were not there initially appear.)

This doctor is standing in front of a patient. He thinks the patient has a bacteria “Whosis Coughus” and that Whosis Coughus is sensitive to Penicillin. But it may be he is wrong and the patient might, instead or in addition, have Buggus Baddus, which needs a different antibiotic.

So the doctor has to choose.

If you believe in evolution then the doctor should give Penicillin. That is likely to help this patient and avoids the bad effect for the community at large that using a broad spectrum antibiotic will result in the evolution of mutant organisms that will harm other people (a lot) later.

If you believe that God created penicillin resistant bacteria and that evolution is a cock-eyed theory then the doctor should give a broad spectrum anti-biotic because that will treat the patient just fine if he has Whosis Coughus and will also cover the possible but less likely case where this patient actually has Buggus Baddus, And there is no downside for the community as a whole in the future because evolution doesn’t actually happen.

So tell me, which do each of you advise the doctor to use - Penicillin or the broad spectrum antibiotic?

Whew Drew! Over 4,000 words to do a little graduate school science review and to miss my main point ;-) This is almost a mirror image to my response to your economics question (where it took me a while to get at your main concern – if I ever did; I'm awaiting feedback there).

Since you spent much time on your background, let me, more concisely, highlight where I agree and disagree.

I would caution the Admiral that using religious reasoning to answer a science question is dangerous.

I am not using any religious arguments whatsoever nor was I the one to bring up souls – they are irrelevant to my point. I did mention a creationist, I thought you'd enjoy the irony of Darwin plagiarizing Blyth to make a naturalist argument. However, the fact Darwin was an intellectual thief has nothing to do with my objections to his theory. I (and many others) reject Darwinism because modern science is showing how untenable Darwinism really is. (Be patient – when you finish this response, including where I define Darwinism as I should have done from the beginning, you'll find us closer than you now believe).

Yes, the scientific method (which I'll distinguish from science since science means many different things to many different people) is one of the most effective tools for learning that man has. Whether you lean toward Popperian or Bayesian views of science, both have points in common. The hallmark of the scientific method is replication. If you cannot perform an experiment (and allow other scientists to replicate the experiment), you are not using the scientific method. The scientific method has been responsible for dramatic progress where it has been applied, but, by definition, it cannot be applied to events that cannot be readily tested and retested. This is why it is laughable to compare Darwin’s theory to the theory of gravity. The theory of gravity leads to many experiments that can test itself and these experiments can be replicated by other scientists. This also explains why some fields of science show rapid progress and others do not. I think we are mostly in agreement on this and I also agree that one of the other hallmarks of science is that you can use it to predict outcomes (which are then tested via the scientific method).

Solipsism, Berkleyism, Christian Science and the Pranskter God

As you have defined them, I do not agree with these concepts either. If you need a label, you may consider me a scientific realist. I'm not a naturalist (one who disbelieves in all things supernatural or outside our universe), but I am a realist (one who believes the universe exists even if humans weren't around to perceive it).

You mentioned the obvious truism that you cannot prove a theory, only disprove failed ones. Gould (and many others) disproved Darwin's original theory, but tried to save the overall concept. More on this in a minute. You said When he [meaning myself] says "Darwinism" I get the impression the Admiral is not talking about Evolution... but may be talking about the divide between inorganic matter (a mix of Methane and Ethane gas) and living matter (a bacteria). No, while that is very tough problem for naturalists, that is not what I meant. When I say Darwinism, I mean those who believe in macro-evolution. This may clear up a lot (and could have saved you hundreds of words about micro-evolution).

Let me define terms. The definition of species is a group whose members may interbreed. Micro-evolution is variation within a species. I do not know of a single scientist who finds micro-evolution controversial. The only real controversy is whether or not random mutation and natural selection simply reinforce and eliminate traits that are already in the genome or if they create new information.

On the other hand, macro-evolution, the creation of new species, is very controversial. This is what more and more scientists, mostly driven by molecular biologists, are rejecting. And this is where people like Johnson skewer biologists who make broad claims about macro-evolution but only show evidence for micro-evolution. Having had many discussions with you, I know you won't make that error in logic now that I've better defined the terms.

Now that I've hopefully made my original point clearer, do you want input on your micro-evolution question?

See comments inline below:
Q> Whew Drew! Over 4,000 words
Drew> Yeah. I was trying to keep it brief [G]

Q> because modern science is showing how untenable Darwinism really is. (Be patient
Drew> OK, I am being patient :-)

Q> If you cannot perform an experiment (and allow other scientists to replicate the experiment), you are not using the scientific method.
Drew> I am suspicious of what you are going to say, but I am still being patient. (Patient is not one of my big strengths).

Q> This is why it is laughable to compare Darwin’s theory to the theory of gravity.
Drew> Uh, what is the difference? But I am still being patient.

Q> Gould (and many others) disproved Darwin's original theory, but tried to save the overall concept.
Drew> Well, no. Gould didn’t say Darwin’s theory was wrong. He said it only covered some cases. That was why I chose Newton/Einstein example.
Darwin explains why there are different species of finches in the Galapagos and why the horse got longer legs and became faster. Gould explains why dinosaurs disappeared entirely so finches and horses could have a chance to populate the earth.

Q> When I say Darwinism, I mean those who believe in macro-evolution. This may clear up a lot (and could have saved you hundreds of words about micro-evolution).
Drew>Until just then I had never heard of either macroevolution or microevolution. Nor have I ever met any biologist who uses either term. I do understand what you are saying. But I don’t see any distinction between the two (they have the same molecular mechanism). But to discuss that I need to make sure we are on the same wavelength about a few other things.

Q> Now that I've hopefully made my original point clearer, do you want input on your micro-evolution question?

Drew>No, I am more interested in:

a) Do you think that because paleontology deals with the past it is not a science. I.e. you can’t come up with a theory, then test it against new data? That is what I suspected back there. More on that depending on if you say yes or no.

Sidebar: The important thing here is making the prediction, _then_ getting the new data. You can’t look at the old data and make the theory based on that old data, and say the theory fits the old data which you already had. That isn’t predictive. But the data can be something that happened a long time ago, just so you didn't have it before you made the theory. You can think there was a Big Bang, predict that if there was a Big Bang something would have happened (something you hadn’t looked at before), then build a device to look for that thing and see if it did or did not occur (12 billion years ago). And other scientists can build a similar device and see if they can see that too.

b) Species: Do you think new species appear ever, or that all the species have always been there? (Discussion goes different ways depending on which. I think new species appear during the course of time). Or do you think there is a continuous creation going on in which God is constantly making new species?

c) Extinction (related to b above). Do you think that is a biological process or something divine.

d) Do you think we are wasting bandwidth and creating Mass Internet Boredom? We can take this to Email if you like.

I wonder what would happen if I successively bred strains of staphylococcus such that some were vancomycin resistant? If I succeeded, would that prove evolution, sans supernatural intervention, to your satisfaction?

J
Who might find publishing a little difficult in these circumstances...

50 years from now the big metaphysical question will be the same as it was 50 years ago: why is there something instead of nothing.

Sadly, I think the physical physicists will still be stymied by the nature of the strong atomic force: what holds the nucleus of an atom together so tightly?

Time, I forgot time:

The last thing I would need to know (from Q) is about time. Here is my view:

This universe began about 12.5 Billion years ago. The sun and solar system are about 4 billion years old (the sun is a third generation star. That will be important if we get around to that point. The atoms that make up the sun (and you) were in two previous stars). Life has been on earth for about 3.5 billion years.

Is that about your time scale? I don't care if you think life has been on earth for 3.0 billion, not 3.5 billion but if you think the real number is around 100,000 there is another huge chasm we will both fall in if we discuss this.

(And there is Vancomycin resistant Staph Aureus)

A Paleontology Theory:

Here is a good example of a "good" (testable) theory in the field of paleontology.

Luis Alvarez (a physicist) and his son, Walter (a geologist), thought that maybe what caused some of the great dyings, and particularly the one that killed off the dinosaurs was an asteroid hitting the earth.

The details were the asteroid kicked a lot of dust into the upper atmosphere, it got colder and darker and most of the plants died, then most of the animals. We are talking a Big Explosion here as physicists use the word Big. Not like a 100 megaton bomb. Huge. The crater is about 350-400 miles across (we now know where it hit, in the Gulf of Mexico but I digress).

Since I have already digressed let me do a sidebar on strata so we will all know how I am using some words. I think the rocks on the earth are laid down in layers (strata) and that the lower layers are older than the newer ones (the newer ones were laid down on top after the older layers had formed). Anyone who doesn’t think that is how strata form, raise your hand)

Alvarez, being a physicist knew that the elements found on the earths surface and in asteroids are different. For example iridium is rare on the earth’s surface, and more common in asteroids. He predicted that in the layer laid down at the time of the putative asteroid strike you would find a thin layer of Iridium. He also predicted that you would find dinosaur fossils below the layer of Iridium (they were alive before the strike) and you would not find dinosaur fossils above (superficial to) the layer of Iridium because there were no more dinosaurs after the strike ("after" in geological terms. They all died before the layer of rock could record that another 100,000 years had passed).

Note some things about this theory:

They predicted something that people would find. Up to then no one had looked for that iridium layer. He was not using old data to make a theory and testing it against that same set of data. He was saying what would be found if new data was generated.

They did _not_ “do an experiment with an asteroid” and (SPCA please note) no real dinosaurs were harmed in the course of this experiment. They predicted what you would find if an asteroid had, in the past, crashed into a planet and also predicted a temporal relationship between that crash and the exodus of dinosaurs from the stage.

You can make predictions that can be tested and you can determine if your theory is correct without killing any dinosaurs. Astrophysicists make predictions about stellar evolution, then prove and disprove those theories all the time. And they never actually make a star out of a cloud of dust and gas.

So people went and looked and, lo, they found the Iridium layer. (they also found, once they were thinking to look a lot of other stuff. Fused quartz and little little glass beads and other stuff you would see if a huge explosion occurred and showered the entire surface of the earth with the melted droplets it created.)

And people have looked all over the world and they have never found (so far) a dinosaur fossil above that thin layer of iridium.

So the theory was “good” because you could test it and it has held up so far. People are continuing to look (because if you find a fossil a little above that layer you will have disproved Alvarez, you will be really famous and you will have provided jobs for lots of paleontologists who will now have to come up with another explanation for the demise of the dinosaurs).

This hasn’t _proved_ the dinosaurs were killed by an asteroid strike. But no one has been able to disprove it.

(Yes, I know there is another theory, that the dinosaurs were already extinct a tiny bit before the asteroid hit, but that isn't the point. The point is that you can come up with testable theories in paleontology).

So you actually can test a theory about events that occurred in the past. Astrophysicists do that all the time about events that occurred billions of years before the sun even formed.

(1) Drew said "This universe began about 12.5 Billion years ago." Yet, that statement is far from certain. Not saying you're wrong, just not saying you're right. Consider Young Earth theory.

(2) Aunt Jane is often late for family dinners. People theorize that she has control issues. This can be tested by generating new data in the form of having a family dinner, to which people predict she will be late. Sure enough, she is. People declare she has control issues. HOWEVER, that test is incapable of testing why she's late. It can only test that she IS late. I'm sure we can agree that dinosaurs are all gone, and I'm sure we can agree that there was a big explosion. It requires blind speculation to link the two.

To Lucy (1):

I have never heard of a Young Earth theory. When you say the 12.5 billion year age for the universe is controversial do you mean "controversey as to 13.0, 12.5 or 12.3 Billion" or do you mean "Maybe only a couple of million years".

If you don't agree with that time scale within an order of magnitude then any reasoning made from data is going to go nowhere.

For example (remember Q asked about data disproving theories about what happened in the past. And I keep using Astronomical data to a) avoid the emotional problem if I use geology/biology and b) because astromers, like geologists, deal with data about what happened long ago.)

Suppose I say "I am looking at light from a star that is 9 billion light years away. And I know that light takes 9 billion years to travel 9 billion light years. So I am looking at what stars were like when the universe was only 1/4 it's current age (the first generation stars were different than the current stars)." (That sort of reasoning is similar to "looking at a rock that is from back when the earth was only 1/4 its current age")

If the audience is going to say "You are not looking at a star as it was 9 billion years ago. God created that star only 1 million years ago. And God created a stream of photons between that star and your telescope ie the light hasn't actually been traveling for 9 billion years, God created the stream light particles between me and the star at the same time he created the star in order to test our faith" then we are not going to get anywhere talking about 9 billion year old stars nor about 2 billion year old rocks.

To Lucy (2):

Regarding the "blind speculation"

Here is the point about reasoning out what the universe looks like by science (ie by the theorize-test theory-revise theory-test new theory algorithm) Alvarez came up with an idea and a way to test his idea and possibly prove that the idea to be wrong. So the speculation isn't "blind". It is testable.

You can't ever prove it right, but you can prove it wrong.

Remember too I said that the fact that despite the fact there was an asteroid strike and the fact the dinosaurs died does not mean all paleontologists say the dinosaurs were done in by the asteroid.

Here is the minority view: The dinosaurs were on the way out already (reasons if you want. I am trying to keep this short, honest.) The last dinosaur species went extinct a little before the asteroid hit ("a little" in geology time). The people who hold that do agree the asteroid hit, and to agree it caused a mass extinction of many species (lots more than the dinosaurs vanished at the time of the asteroid hit. Most life is in the oceans and there was a mass extinction on land and sea and lots of different species after the asteroid strike). This minority view _does_ agree the asteroid caused one of those Mass Extinction events (it wasn't a big one, BTW. There were much bigger ones earlier in the earth's history). They just don't think the dinosaurs were around to "particpate in the extinction" as it were.

So if you want to hold that view (that the dinosaurs were gone a million years or so before the asteroid hit) you need to come up with a testable way to prove that is wrong.

That's what scientists really to with their time. They don't "just speculate" but they speculate in a structured way where the speculation can be tested against the universe and tossed out if it fails. That is the Big Difference between an astrophysicist and a philosopher for example, when both "speculate" about where we all came from. The philosopher thinks and only is worried about internal consistency of his thinking (mathmeticians are like the philosopher in that regard). The astrophysicist has an outside referee.

To Lucy (1) Addendum:

(To Q, is there a way for me to edit comments once I posted them?)

To keep things tidy and make sure we are all (pretty much) understanding what the terms are (this discussion is really more orderly than it looks) that discussion about the age of the universe and the distance light has traveled is what I would term "The Prankster God" as I used that earlier.

I say the universe is 12.5 billion years old. I say the reason I pick that number has to do with a) how far light has traveled (if I can see something 11 billion LY away that thing was there _at least_ 11 billion years ago) and b) by the size of the universe and its rate of expansion.

If you say "The light didn't travel the whole distance, it was created part way along the path. And the universe didn't expand all that far, it was created expanded partway." then there is nothing science (the theorize-test-revise theory-retest) mental process can do. Any experiment that one can devise to test a theory can have God reach into it and give a capricious result just to test our faith.

Lucy used the words "Speculation" and "theory" in her post. And we keep getting tangled up in using words differently. There are different kinds of theories (the "Defense theory" of who really killed Mark Peterson's wife" for example) but I want to talk about one particular kind of theory, the "theorize-test to see if I disprove it - new theory" sort of reasoning science uses so let me call that "a scientific theory" (one that you can use in the reasoning that scientists started using in about 1500-1600). "Speculation" sounds pejorative but you can call something a philosophical position, a view about the nature of things or something like that. This speculation/world view differs in that it is _not_ testable.

I have not, as I said, heard before of the Young Earth Theory but if this is a scientific theory (as opposed to a philopophical postion) then it should be testable.

Lets say I say the earth is 4 billion years old (the "Old Earth Theory") and you say the Young Earth theory says it is only about 1 million years old (is that what it says?) You cannot convince me the Young Earth theory is true because you can't prove a scientific theory (only disprove it) but you can convince me the Old Earth theory is wrong, needs to be discarded and the Young Earth theory is better.

Tell me some test, something you and I can both observe that will be "A" if the earth is 1 million years old but "B" if the earth is 4 billion years old. If you can come up with that test, and if we all observe A then the Old Earth theory goes the way of the heliocentric universe and your view is the new working hypothesis.

I am not saying that is the only way people reason. It clearly isn't I _am_ saying that is how you have to reason if you want to say it is a scientific theory.

And I am saying the scientific method are the best way (no other way is even in the same ball park) to find out the nature of the universe. That is what it is designed to do and what it tests itself against.

Scientific method is not suitable at all to reason your way to religious beliefs.

Drew, here is a pretty decent yeC (Young Earth Creation) summary:

http://www.asa3.org/ASA/education/origins/ye-cr.htm#top2

If you google Young Earth Theory, you'll find a ton of stuff. Personally, I was interested by the idea offered at http://www.icr.org/pubs/imp/imp-242.htm about using the Earth's magnetic field to speculate on actual age of the planet (although I did wonder about the accuracy of measuring fluctuations thousands of years ago).

Another set of articles by an environmental biologist in favor of YeC is http://www.answersingenesis.org/search/default.aspx?qt=Young+Earth&loadpage=query.html&charset=iso-8859-1 He strikes me as slightly more reliable and mainstream. (He also has a series of articles on Evolution that might inspire you :)

Wow! What a lot of comments, wish I didn't have to work. I'll answer as many points as I can given my time constraints - but you good folks keep posting faster than I can respond :-) In order to prevent ridiculously long posts, I'll try to answer most points with individual comments (that will also help my time management).

I'll first talk about Drew's sidebar because this will give Drew something to talk about while I read the other comments.

Sidebar: The important thing here is making the prediction, _then_ getting the new data. You can’t look at the old data and make the theory based on that old data, and say the theory fits the old data which you already had. That isn’t predictive. But the data can be something that happened a long time ago, just so you didn't have it before you made the theory.

I'm not as sold on this as you, but I freely admit that many (and probably most) scientists hold that the theory must predate the evidence or you eliminate much of the value of the scientific method. That is why I do not understand your great respect for Gould. Gould's theory of punctured equilibrium was completely data-driven. Darwin's theory predicted a slow change. The fossil record did not support this. Knowing the data in advance, Gould came up with the punctured equilibrium theory. Why do you respect Gould's theory since it was driven by the data? (In fact, it was proposed as a defense against those who were using fossil data to falsify Darwin's theory, hardly the epitome of theory driven research).

Now you talk about this while I try to read the other comments on my lunch break. :-)

Do you think we are wasting bandwidth and creating Mass Internet Boredom? We can take this to Email if you like.

Judging by the number of comments (even if we don't count yours and mine), others are quite interested. Besides, I’m paying for the bandwidth – go for it. This will save us (and others) from having the same conversation 2 years from now.

New Species

Jim asked I wonder what would happen if I successively bred strains of staphylococcus such that some were vancomycin resistant? If I succeeded, would that prove evolution, sans supernatural intervention, to your satisfaction?

This would be a case of micro-evolution and I agree that this is non-controversial (i.e., does not require supernatural intervention). As I said before, The only real controversy is whether or not random mutation and natural selection simply reinforce and eliminate traits that are already in the genome or if they create new information. Your question provides a very good example of this. Let's assume you successfully bred a new strain of staphylococcus that was now vancomycin resistant. In theory, without assuming any intelligent intervention, there are three ways this could be done. (I am also assuming you have isolated these bacteria so that other, already resistant bacteria, could not exchange extrachromosomal plasmids – one of the primary ways bacteria, in effect, trade resistances with each other).

1) If information already existed in the staphylococcus genome that would allow some strains to be vancomycin resistant, natural selection alone would create a strain of vancomycin resistant staphylococcus. This is the most probable outcome.

2) If such information did not exist in the staphylococcus genome, then the organism must mutate or die. If a mutation occurred, the most probable mutation would be one that deactivated part of the staphylococcus genome. For example, let's assume vancomycin attacked staphylococcus by exploiting its thin cell wall. A random mutation might turn off the chromosome that limited cell wall growth. While this would shorten the absolute life-span of the staphylococcus strain, it would increase the actual lifespan of the bacteria in the presence of vancomycin. This mutation is unlikely, but given the vast numbers of bacteria, it is certainly foreseeable that such a mutation might occur and breed a strain of vancomycin resistant staphylococcus.

So far, both example are non controversial by all theories under discussion. The third example is more controversial.

3) A serious of random mutations resulted in an improved staphylococcus that now had new information in its genome. This new information was not in the original genome, nor is it a matter of turning off existing information (e.g. not a defect with positive consequences), but is a totally new way of handling the vancomycin problem. This example is very controversial and I find it extremely unlikely. If you could find such cases, that stood up over time (i.e., no one latter discovered that the change was actually part of the original genome that no one originally understood), then this would be a necessary step toward a viable theory of macro-evolution. If this can not be proven for simple variation within existing species, then the case for macro-evolution completely falls apart (which is why most of the micro-biologists I know do not believe in macro-evolution).

Well, that's it for now – will revisit these comments when time permits.

Re the Young Earth URL:

I read (real fast) that Young Earth reference. I did not see a testable way to prove the universe or the earth is "young" in gelogical terms but tell me if I missed it. I did see the "apparent age" thing (as I understand it what I described as God creating a star yesterday, 6 billion LY from me, and also creating a stream of photons 6 billion LY long so I could see the star).

But no testable theory.

Micro-Macro Evolution:

As I said, I don't buy this. I don't see any difference. Hmm, how can I say this as succinctly as possible:

1) I picked the Horse/Burro/Zebra thing with care. Clearly a Horse and a Zebra are different species. A Horse and a Burro are at the dividing line of a new species. That is a snapshot of the two going over the line, in the act of diverging. So it is not "My Species or not". There are "Almost not my species" and "just barely not my species".

2) We need to discuss bacterial genetics a lot more. I need to see how to distill that down. Bacteria have an asexual process (one bacteria divides in two) and a sexual process (two bacteria exchange DNA without dividing). That "exchange DNA" thing is pretty common. You are doing it all the time in your own cells. Including with other species. (That's how retroviruses work, among other viruses).

So in bacteria, too, there are different/more different/really different genomes. And it is all the same molecular mechanism. Eventually the genome is so different we say "new species" but that new species can still trade DNA with other bacteria (or with you depending on the bacteria and the intermediary carrying the gene).

See next post though

What I really need to know (from Q) to see which way to go is:

Do you think new species do continue to occur through time (in other words all the species weren't there at once). I am going to presume you think "yes", that the hippopotamus was not around when the pterodactyl was.

Do you think the DNA/genes are what give the instructions (mostly, there is a maternal facto too) to make an individual organism (I am going to assume you think yes)

Then we are quickly going to get to:

I think the changes in the DNA are perfectly explainable by normal rules of chemistry.

Q thinks the tiny changes are explainable by chemistry but the changes that mean a horse and a zebra are different species (or a new species of bacteria is now there) require God to "adust" the DNA (outside the normal rules of chemisty) to make that new DNA, new genes and new species.

Is that about right?

That is sort of a dead end. I can't think of any way to look at a gene sequence and say "That change there, C for A, was due to keto-enol tautomerization" (a random statistical event. There are reasons for mutations but I pick that one because it _is_ random. A nucleic acid base spends most of there time in one configuration but a tiny fraction in the other, and by chance, sometimes the replication of the new strand takes place when they are randomly flipped so the copy-strand doesn't match the template strand) but this second change from C to A, which finally was just enough to push the zebra over the divide and finally made it a new species, was not a random flip of the electrons to the "keto" position, but God urging them to flip just at the right moment.

Is that where this is going?

The medium sized horse and the panda’s thumb

I want to get away from genes, DNA and organic chemistry for a couple of reasons. I suspect most here are not chemists, and the original question (“Is Darwin nuts?”) can be addressed without genes or chemistry. His theory didn’t mention them.

What Darwin said was that one species can gradually accumulate different qualities (“taller” is one). And “taller” doesn’t necessarily require a new “tall enzyme gene”. It may be less quantal (more of a small change in degree rather than a new quality entirely). So what he is saying is one species can slide into another.

What I gather Q is saying is that there is a divide where God has to intervene to make a new species.

Look at the medium sized horse. There were small horses (about 18 inches high). If God wanted to make a big horse with long legs, why not just make one? Why all these fossils of horses that are gradually larger, eventually getting to the modern horse?

Darwin’s theory would say “Because you can’t just go small horse -> Sea Biscuit.” (that is a famous race horse for those of you less than 50 years old). You can only make small modifications starting with what you already have. God could do anything he wanted (Lobster -> Mike Tyson). No limits on “where can I get from here”. You just could go to the end point. But Darwin's theory says you can only modify what you have. And there are all these intermediate sized horse fossils. . .

The Panda’s Thumb is the name of a book but also of the lead essay in that book, by Stephen Jay Gould. The point of the essay (I encourage you to read it) is a little subtle. Subtle in spite of Gould saying it about 30 times. It is subtle because it is not the conclusion you expect.

Most land animals have 4 “regular digits” and a thumb (not all animals. You can read “Ten Little Piggies” also by Gould if you want to know a lot about the hand. (I happen to spend most of my professional life dealing with the structure of the hand. In my youth I spent most of my professional life investigating the nature of genes and DNA. But you probably guessed that [G]).

Thumbs are nice because they are a little different than the other 4 digits and help you grab some sorts of things. But you don’t necessarily need one. Horses don't. If you have no occasion to grab things there is no selective advantage in having a thumb and you lose it (I don't see why God would take away a gene just because you don't use the gene product. But then I don't think that is how speciation works). If the thumb is just excess baggage you lose it. Horses lost their thumbs and so, at one point, did ancestors of pandas.

Then the panda-ancestors changed job descriptions and began to eat bamboo, rather than just walk around on the forest floor. So they needed thumbs again.

Now if you hold to Q’s hypothesis (God makes genes for things the species need as special projects) it is no problem. God already knows how to make a thumb gene (he used it in the panda-ancestor). So he just adds it back.

If you hold to the “you have to modify what cards your gene-pool has dealt you” theory (Darwin) you can’t do that. You discarded the thumb gene long ago.

So panda have a protruberance on the “thumb side” of their paw. But if you look at the bones used to make that “thumb” they aren’t the same bones the panda-ancestor (or you, assuming you are a primate) use. They are a highly modified carpal (a different bone, a wrist bone, not a finger bone).

The panda did not just “use the perfect design thumb gene" that God already knew about. The panda had to modify what he had at that point in evolution.

It is those compromises and half-way steps that are one of the pieces of data to support Darwin’s “gradual modification of what you have by selective advantage” theory rather than a “make a new gene if you need a new species” theory.

Medium sized horses and crude thumbs made out of a distorted wrist bone. Hmmm . . .

Aristotle's Horse

Discussing "Is Darwin right or wrong" is not a subject that can be settled by debate. You can settle issues in mathematics or philosophy by reasoning through the proposition and showing it is inconsistent. For a scientific hypothesis (same as "theory" but I want to get away from "theory" as used in "Young Earth Theory" for example) the test is not whether it is consistent but whether it predicts the observation made in the real world.

You can make a theory that liquids increase in density as they cool. There are very good reasons for generating that hypothesis. A thermodynamic one for example. The hotter molecules jiggle more and will spread further apart. And it holds for almost all molecules in liquid phase.

Then you measure water and you find that water increases in density down to 4 degrees C, but then starts _decreasing_ in density until zero degrees C. You are really unlikely to predict that. It isn't logically consistent. Why is water weird? But that's the observation. Now you need a different theory of how molecules interact in the liquid phase that includes water behaving differently than most other substances.

Coping with the universe is your own problem, as Tricia MacMillan (Hitchiker’s Guide to the Galaxy) put it so elegantly, not a problem for the universe. It actually doesn’t care if you are surprised, wouldn’t have done things that way, find it inconsistent, illogical and annoying.

There is a story, likely not true but real old (dates to about 350 BC) regarding Plato and Aristotle. (And I am not looking up the details of the numbers. You'll get the point even if the real story has different numbers).

The brightest minds in Greece are gathered at the Academy. Plato decides that the topic for discussion today will be "How many teeth does a horse have?"

One philosopher says that man has 32 teeth, and man is superior to the horse (for example men are philosophers) so a horse, being less perfect, would have only 28 teeth. "Interesting," says Plato.

Another philosopher says that man gets nourishment not from food alone, but also from philosophical discussion with other learned minds. So a horse, having only food as nourishment, would need more teeth - 36. "Very interesting," says Plato.

Aristotle gets really bored during all this. He drums his fingers on his couch, then eventually gets up and wanders out of the room to Plato's great annoyance. So when Aristotle returns Plato calls on him (sounds like professors you knew, huh?).

"Aristotle, tell us, how many teeth has a horse?"

"Twenty-four" says Aristotle.

"An interesting conjecture. And what argument will you give us to support that number?"

"While you were droning on I went out in the street and counted the teeth of a horse."

That's the difference between philosophy and mathematics, which use deductive reasoning and science. Deductive reasoning starts with first principles (a postulate, an assumption) and builds a system on that first assumption. What counts is that none of the reasoning contradicts other parts of that same chain of reasoning.

Science doesn't give a hoot for consistency, logic or clever arguments. All that counts is "does that fit the observations?" This makes science really good at letting us learn the nature of the universe. That's the only thing science ever measures itself against - the nature of the universe.

So if you want to propose that Darwin’s theory is wrong and use a philosophical or theological reason, I will tell your philosophy or theology are just fine as philosophy and theology and quite your own business. But if your theology or philosophy contradict Darwin’s Origin of the Species that has no effect whatsoever on its validity as a scientific hypothesis (which is excellent). Nor on the nature of the universe (which science, not theology or philosophy is good at discovering).

The _only_ thing you can do to overturn Darwin’s hypothesis as incorrect science is to come up with an observation (not an argument) that contradicts it.

Aristotle's Horse

Discussing "Is Darwin right or wrong" is not a subject that can be settled by debate. You can settle issues in mathematics or philosophy by reasoning through the proposition and showing it is inconsistent. For a scientific hypothesis (same as "theory" but I want to get away from "theory" as used in "Young Earth Theory" for example) the test is not whether it is consistent but whether it predicts the observation made in the real world.

You can make a theory that liquids increase in density as they cool. There are very good reasons for generating that hypothesis. A thermodynamic one for example. The hotter molecules jiggle more and will spread further apart. And it holds for almost all molecules in liquid phase.

Then you measure water and you find that water increases in density down to 4 degrees C, but then starts _decreasing_ in density until zero degrees C. You are really unlikely to predict that. It isn't logically consistent. Why is water weird? But that's the observation. Now you need a different theory of how molecules interact in the liquid phase that includes water behaving differently than most other substances.

Coping with the universe is your own problem, as Tricia MacMillan (Hitchiker’s Guide to the Galaxy) put it so elegantly, not a problem for the universe. It actually doesn’t care if you are surprised, wouldn’t have done things that way, find it inconsistent, illogical and annoying.

There is a story, likely not true but real old (dates to about 350 BC) regarding Plato and Aristotle. (And I am not looking up the details of the numbers. You'll get the point even if the real story has different numbers).

The brightest minds in Greece are gathered at the Academy. Plato decides that the topic for discussion today will be "How many teeth does a horse have?"

One philosopher says that man has 32 teeth, and man is superior to the horse (for example men are philosophers) so a horse, being less perfect, would have only 28 teeth. "Interesting," says Plato.

Another philosopher says that man gets nourishment not from food alone, but also from philosophical discussion with other learned minds. So a horse, having only food as nourishment, would need more teeth - 36. "Very interesting," says Plato.

Aristotle gets really bored during all this. He drums his fingers on his couch, then eventually gets up and wanders out of the room to Plato's great annoyance. So when Aristotle returns Plato calls on him (sounds like professors you knew, huh?).

"Aristotle, tell us, how many teeth has a horse?"

"Twenty-four" says Aristotle.

"An interesting conjecture. And what argument will you give us to support that number?"

"While you were droning on I went out in the street and counted the teeth of a horse."

That's the difference between philosophy and mathematics, which use deductive reasoning and science. Deductive reasoning starts with first principles (a postulate, an assumption) and builds a system on that first assumption. What counts is that none of the reasoning contradicts other parts of that same chain of reasoning.

Science doesn't give a hoot for consistency, logic or clever arguments. All that counts is "does that fit the observations?" This makes science really good at letting us learn the nature of the universe. That's the only thing science ever measures itself against - the nature of the universe.

So if you want to propose that Darwin’s theory is wrong and use a philosophical or theological reason, I will tell your philosophy or theology are just fine as philosophy and theology and quite your own business. But if your theology or philosophy contradict Darwin’s Origin of the Species that has no effect whatsoever on its validity as a scientific hypothesis (which is excellent). Nor on the nature of the universe (which science, not theology or philosophy is good at discovering).

The _only_ thing you can do to overturn Darwin’s hypothesis as incorrect science is to come up with an observation (not an argument) that contradicts it.

Drew,

I just don't understand how you can compare evolution to gravity. How can you possibly test Darwin's theory about horses/big & small/zebras/burros? Tell me how I could disprove it? Is there a way? If not, I don't think it qualifies as science. Maybe scientific history or something, but definitely not the same thing as gravity.

To Luke:

Show the universe is only 100,000 years old (the Young Earth theory) and you have excellent evidence Darwin is wrong.

Show that all the species existed from the beginning of life on earth (whenever you think that was. 3.5 billion years ago or 1 million years ago.) Find a fossil human or modern horse in the same strata (layer of rock) as a trilobite (a crawly thing that predates the dinosaurs by a lot).

Find either of those and Darwin is in trouble.

Re "historic sciences". What about astrophysics and cosmology. Are those different? Do you think the Big Bang happened? Same thing. There is evidence scattered around in the present we can see that you can explain by the Big Bang. There are things you can look for that, if found, would mean the Big Bang hadn't occurred. But we don't see those things. But no one actually starts a new universe with a Big Bang to test the idea. (If we hadn't found the cosmic background radiation we would probably have gone back to the drawing boards for example).

As a personal question: Where do you think the iron in your own personal red blood cells came from? I think those iron atoms came to exist by going through the cores of two stars (in succession). Hydrogen to middle atomic number elements like nitrogen and oxygen, then those middle atomic number elements happened (after the first star went supernova) to wind up a long time later in the core of another star that likewise went supernova and converted the middle-sized elements to heavy elements (iron for example). The reasoning is similar. No, I have never seen an experiment where a scientist made a supernova and put oxygen in the core of that star. (And if you want to get a gut feel for how old the universe is, every iron atom in your body has been through the core of two successive stars since the Big Bang. Time is really long in our universe at the moment.) Find a nuclear reaction that goes Hydrogen -> Iron without the intervening steps and that idea goes into the dustbin.

The reason I keep coming back to cosmology and astrophysics is they are also sciences that deal with looking at what we see today and figuring out what happened in the past. And they tend not to have the emotional/religious overlays of the origin of the species. But you are still looking at what you see today to try to figure out what happened in the past.

More on that Iron Atom thing:

The point of that (I keep being caught between "keep it short" and "explain what you mean") is this:

I am going to tell you the history of an atom in your body. It is the history of the iron atom in the hemoglobin molecule that just delvered the oxygen molecule to your brain that let you see the period at the end of this sentence. (That period there)

After the Big Bang there was only Hydrogen and Helium. Some hydrogen was in the core of a star that was large enough to go nova. When the star went nova, that Helium and hydrogen was trasmuted to middlesized (teens) atomic number elements like oxygen and nitrogen. Those oxygen and nitrogen atoms (by gravity) eventually (a long time later) got swept up in the gas cloud that formed another star. Not just any star, but one large enough to go nova again (not all stars are big enough). When that second star went nove those O and N atomes underwent a nuclear reaction making an atom of iron (are you starting to get a feel for how large space is and how long time is for all this to happen to happen, as it were?). The iron atom then floated around for a while, and wound up in another gas cloud that coalesced to form our sun and the sun's planets. But that particular atom wound up in this one planet, then in your body.

I wasn't here when the second nova happened. You weren't either. And the iron atom in question wasn't there until the nova actually occured. But I am telling you all this (which happened a long time ago in the past) because:

a) there is lab evidence reactions like that happen (like there is lab evidence DNA can mutate)

b) I can see stars of various age in the sky. Some (the really old ones) are only H and H2. The later ones have O and N. The newer ones still have Fe (iron for those of you from Rio Linda).

You _could_ disprove that theory of what happened in nucleogenesis billions of years ago. For example, you could show me a first generation star (one formed from the original gas cloud made in the Big Bang) that had Iron in the spectrum of the star.

Then I would say "That theory of nucleogenesis is bunk. It works in the laboratory but it didn't happen in that star so there must be some other way to get Fe atoms."

That is looking at data from the past of the universe to figure out what happened to happen.

Similarly, if you find a rock that dates from the early stage of the earth (right after it cooled to solid, say) and in that rock you have a trilobite fossil, a medium sized horse fossil, a zebra fossil a neanderthal fossil and a homo sapiens fossil I will say "Darwin is bunk and although I can mutate DNA in the lab, what happened in the past was some other process."

There are ways to try to determine how the universe got to be the way it is right at the present.

I just made up the term scientific history, meaning that you need to have some sort of scientific education in order to understand it. I won't pretend to understand what you are talking abut concerning iron. But I don't really see how it makes your point.

Evolution as it pertains to an origin of a species or Big Bang theory or whether or not Washington fought in the revolution untestable using the scientific method. You can look at the data and draw a conclusion, but you can't ever replicate it.

If I don't believe in gravity I can test it with my own apples and feathers or whatever. If I don't believe in cold fusion I can replicate the scientists conditions in my own lab and see if it works. If I don't believe that zebras evolved from horses I can't recreate the situation and observe it for myself.

I'm not saying that there isn't good evidence for a Big Bang, or that iron doesn't come about as you say it did. But you can't show it to me. You can't test it in your own lab. It's speculation. It's probably a well thought out and well educated speculation, but it's still speculation.

Maybe there was a big bang. You say the background radiation would suggest it. Maybe we're in a galactic microwave owned by huge aliens. I don't know. But you can't reasonably put evolution in the same category as gravity. If you could we wouldn't be having this discussion. You would just say, "go set up these conditions and evolve a horse in your garage."

History books are always changing, revealing new things about the past. I was taught that Washington was a general in the revolution. Historians believed it because of some evidence they found, books or archaeological or otherwise. If someone next week found a book by Jefferson that said Washington died when he was 12, we would have to change our perception of history, or at least reexamine it. That is what big bang theory, evolution, creationism, is to me. It's not subject to scientific analysis. It's subject to a historic analysis, but it's just not the same thing as gravity or light being a wave or a particle or the quantization of energy.

To Luke, Mostly:

You are saying, as I understand it, you can’t use the Scientific Method to figure out what happened in the past. Sure you can. You make a hypothesis. Then you look for data that contradict that hypothesis. If you find such contradictory data you have to scrap (or modify) your hypothesis. The more different kinds of data you get without contradicting your hypothesis, the more confidence you have in the hypothesis.

There are lots of things science studies which occurred in the past. Where stars come from is a good example. No scientist has ever made a star. No scientist has ever watched a single star go through its life cycle. But scientists have a pretty good idea how stars form, age and die.

You may never have seen a single Black Oak grow from an acorn into a sapling, a mature tree and then a dead stump (that takes about 500 years. Black Oak are long lived). But you can walk in the woods, see lots of Black Oak at different ages, and get a reasonable picture of what does happen over those 500 years.

Let’s go back to iron atoms and horses.

I am saying that iron atoms weren’t always there. They didn’t even appear in one step from the stuff (hydrogen) that _ was _ there right after the Big Bang. They evolved (went through some intermediate steps over time.)

And I am saying that horses weren’t always there. They didn’t even appear in one step from the small horses we see in fossils. They evolved by going through intermediate steps (all those gradually larger horses with gradually one dominant toe and all the other toes gradually becomiing more vestigial.

I am saying there are laboratory data for the thing I am saying about iron atoms. Experiments in cyclotrons and linear accelerators.

I am saying there are laboratory data for the thing I am saying about horses. Experiments where bacteria grow (bacteria because I can watch 1000 generations in two weeks) or with naked DNA molecules in solution (not inside a cell) watching the DNA sequence mutate.

I am saying that there is a way to test to try to disprove both of these as historical processes.

I am saying there are old stars and young stars. For example a star I see 8 billion light years away must have been there when the universe was only 1/3 it’s current age. And there are stars that are old based on the fact they have consumed most of their fuel.

I am saying there are old rock layers and young rock layers. For example this layer may be old compared with that one based on the mix of isotopes in it. And for sedimentary rocks (rocks formed in river or ocean silt as it compacts over time. Sedimentary rocks are generally the ones with fossils for reasons that should be obvious) I think that the layer that is higher was layed down on top of the layer below it and therefore is younger (I don’t think the sediment settled out _ under_ the lower layers of rock on the bed of the ocean, but on top of those rocks).

I am saying you can disprove the iron-evolution theory by showing a star that is from the first part of the history of the universe (stars formed directly from the gas cloud left after the Big Bang. If you find a star that formed in the first billion years of the universe and show oxygen and iron in that star you have disproved (by a scientific experiment – measuring the light from a star and looking in the spectrum for iron and oxygen) the iron-evolution hypothesis. But you don’t. You find in the earliest stars only hydrogen and helium. In the second generation stars you find hydrogen, helium, oxygen and nitrogen but no iron. In the third generation stars (the sun is a third generation star. It is “only” about 4 billion years old, having formed in the last third of the time that has passed since the big bang) you find hydrogen and oxygen and iron.

I am saying you can disprove the horse-evolution theory. By finding a rock layer that is “old” (from the time of the small horse with lots of toes) and showing in that same layer (in the rock from that same age) fossils from the middle sized and the large modern horse with few and one toes respectively. There is an experiment you can do (look in rocks from the right age and find a one=toed horse) to disprove the horse theory.

If you do that (for example find a star from the first billion years of the universe with iron in it) I will say “Well, it looks like the Iron Theory is possible, based on the lab data, but even though that is one way that Iron might have been made, there must be another way it has, in fact, been made in the history of this universe because there is iron in stars too young to go through those intermediate steps.

Note that you are disproving not the fact that helium can go to oxygen (a bunch of them fusing) then to iron (a bunch of oxygen atoms fusing). That can happen. But you want to know not what one possible path to iron was, but what path was actually used during the evolution of the universe. So you look at historic data and you could find data to scientifically show that iron, although it could be made that way, was made some other way.

You can do the same thing with a horse – prove that although DNA does mutate in the test tube the horse didn’t form from the small, many toed horse by that method by finding the right fossils.

That test (looking for the star or looking for the fossil) is something I can do, find the iron-in-the-old-star or fossils-of-large-and-small-horses-in-the-same-layer, publish it in a journal, and you can go out and reproduce that (find the fossils or measure the starlight) and confirm my observation.

You +can+ use the scientific method to study what happened in the past.

100% behind your arguments

My only problem (if you wish to call it that) is that, intuitively, I find it hard
to believe that elephants, lizards and humans all evolved from an amoeba or a paramecium.

Correct me if I'm wrong (like there is any doubt of that ;) ), but isn't that the conclusion that you must reach if you take the Theory of Evolution to its penultimate beginning?

To Khobrah:

Hmm, I bet I am taking your statement _way_ too literally. Paramecia and Amoebas are a branch of life that have multiple nuclei per cell. We only have one nucleus per cell. Amoebas and paramecia are related to the rest of life (horses, me) but not very closely. You are more closely related to a redwood tree.

We did not evolve from amoebas nor paramecia. We do have a common ancestor _way_ back. But once they went down the multiple nuclei pathway there was no further common ancestor.

You are talking about the divide where life finally got beyond the bacterial cell (no nucleus, all the chemical reactions in the "same compartment" as it were) to the next level of complexity (nuclei and organelles compartmenting off parts of the internal content of the cell. That lets you run this chemical reaction over here, metabolizing glucose maybe, without the reactants getting into that reaction over there).

They went one way (and may have made the mutaion from bacterial life (no nucleus) to plant/animal cells (nucleus) at a different time than our ancestors. More likely one organism hit on the "nucleus" concept then, real soon thereafter some went down the "Let's divide every time we make a new nucleus" pathway (us) and some said "Let's have several nuclei because our cells are now so much larger" road (the amoeba and the paramecium). Your body's cells are, in general, small compared to a protozoan like a paramecium.

And I don't think "humans evolved from chimpanzees." I think there was a primate at some point in the past which was a common ancestor of humans and of chimpanzees. ("I am not descended from my cousin, but we do share a common ancestor"). I think humans and horses share a common ancestor too. But that was much further back in the past than the common ancestor with chimpanzees. And a common ancestor with E.Coli bacteria. But that was way way back.

There is a difference between "common ancestor" and "descended from."

By the way, the time scale is that almost all the time life was on earth (about 3 billion of the 3.5 billion years) there were _only_ primitive one celled organisms (bacteria basically). This cell nucleus idea is a new concept. And this multicellular organism idea. The height of avante-garde!

Why do I think we have common ancestors? For one thing the genetic code is "degenerate" meaning I can make the same gene product (protein) with any of several different DNA sequences (there are more possible code triplets than there are amino acids if you want a more technical reason). So I could make this enzyme over here with a gene that had any of a number of different DNA base pair sequences. But I tend to use the same DNA sequences as that E.Coli when we make the same enzyme (more or less).

Another reason is that same reasoning I used for proto-horse->zebra and modern horse. You see (in the historic record) so many of the intermediate steps. The one celled organisms, then the early multicelled organisms (The Burgess Shale stuff) then the later multicelled organisms.

And I find it easier to see a way for life to start once, with simple one celled beasts (bacteria) then have those come to be multicellular organisms rather than seeing a second start to life, this second time, after 3 billion years, and have that second start NOT be simple bacteria but be the more complicated multicelluar beasties.

And note I haven't said anything about "soul" here. I don't have anything to say (from a science point of view) about souls. That is not a subject where science has anything useful to say.

Where is God in all this? Personally (and this has nothing to do with science) I think God started the universe (actually probably a lot of them. A "multiverse" if you know the cosmologic term) with a bunch of consistent laws to operate under (gravity, strong and weak nuclear force, electormagnetism etc.) and the world operates according to those physical laws continuously without outside fiddling on his part. But that idea (that God started the whole thing) isn't science.

Khobrah said: "intuitively, I find it hard to believe that. . ."

Yeah. Me too. So?

Let me quote Tricia MacMillan (Hitchikers Guide to the Galaxy) more fully. "We have achieved normality. So anything you still can't cope with is your own problem. Relax."

This Universe actually does not care if you find evolution hard to believe. Evolution happens to be how this particular universe works, however, which is the only question on the table. This Universe also does not care if you find quantum indeterminancy hard to believe (evolution is nothing compared to quantum indeterminancy). Me, I would not have chosen quantum mechanics as the basic (probably only) building block on which to construct a universe. But I wasn't asked.

And you weren't asked if evolution was how you would do things if you were in charge.

The "religion vs science" crowd always bother me for a very basic _theological_ reason. Science actually does describe how this universe works. Then people look at the universe and say "God would never have been so dumb as to do that". Well, he did. Why do _you_ think he made a colossal mistake? He may have had a very good reason for choosing evolution (or quantum indeterminancy) that you just aren't bright enough to see.

It is not your universe. It is not my universe. We both just live here.

And it is not in your job description to _design_ a universe. But if you are a scientist it _is_ in your job description to figure out how this one works.

Deal with it.

If God, for reasons unknown to me, chose to make this universe run the way it is, I for one am not going to tell him he should have made a different one.

>>The only real controversy is whether or not random mutation and natural selection simply reinforce and eliminate traits that are already in the genome or if they create new information.

If I understand you right, when we apply this test to the staph bacterium which we've bred to become vanc resistant, evolution has not occured because the trait was already in the genome like a little homonunculus?

Likewise, if we bred and domesticated wolves over dozen thousand years, selecting for loyalty and obedience, the resulting species would be but expressions of pre-existing canine homonunculii? (homonunculae?)

J

So, with a slight semantic change, my
posit that ALL life evolved from a BACTERIA (or several bacterias) was pretty much accurate.

Now for the $20,000 question:

Where did that bacteria come from?

Was it created by Divine Intervention, alien "seeding", or random chance?

Can we create bacteria in a lab?

Also, I've read studies where we have "tailored" bacteria to adapt to high-pressure environments and/or other hostile conditions.

Going back to the original postulate that bacteria are the original source of life on Earth, I don't think it all that far-fetched that some aliens (either trans-dimensional or extra-Milky Way) "seeded" tailored bacterium onto the Earth 3+ Billion years ago. They couldn't have been from the MW - it is too young for that level of development.

As I see it there are only 3 choices:

Divine Intervention
Alien Intervention
Pure, Blind Chance (unless you consider Luck to be a Goddess, then you are back to 2 choices)

I don't see how any of the theories of "first life" are disprovable.

There is no record of prehistoric bacteria is there?

Oh Drew, BTW, you really need to find a better source of quotes. Using a fictional character to illustrate your points is a bit counter-productive.

Can't you Scavenge up something better? ;)

Khobrah wrote:
"Now for the $20,000 question:
Where did that bacteria come from?"

My view or Darwin's view?

My personal opinion is that crossing the divide from a bunch of chemicals to a self replicating collection of chemicals, walled off by a little sandwich bag (cell membrane) from the rest of the chemicals in the environment was a process that occured in stages by the natural laws that operate all the time. I don't think God had to reach in and do some direct intervention to get that to occur.

So of your three choices I pick "pure blind chance" in the sense that chemical reactions occur by "pure blind chance" (kinetics of molecules happening to collide) but with the understanding there are the consistent physical laws regarding how those molecules interact when they do collide. Those laws weren't changed, in my opinion "just this once" to get the result God wanted.

Why don't I believe God intervened directly? Scientists say that ideas are "fruitful" (they lead to more useful ideas) or "not fruitful" (they lead nowhere. Scientist are not big on poetic nomenclature). Working out what the universe is and how it got that way by assuming there is some law is operating consistently has been "fruitful". The reasoning scientists use has admirably expanded our knowledge of the universe since 1600 and allowed us to manipulate the universe to our great advantage.

Saying "That was a one off miracle" every time you are stumped is the ultimate "not fruitful." You can _always_ claim that. It doesn't get you anywhere. That is the science reason.

There is another reason. I can't imagine God needing to do all that patchwork. That is what bothers me with the Prankster God idea, of which "let me add life by a miracle here" is a variation. You have God running around doing little touch ups in the corners every time you notice something in the corner you can't explain. That is a pretty tacky God to my mind.

Darwins idea? Darwin's Origin of the Species doesn't address the issue of the origin of life from inorganic matter at all. His theory is about how one species comes from another, already existing species.

Re the quotes: I use 'em from wherever I find them. I actually find Conan the Babarian, Hitchikers Guide and The Godfather all provide pithy comments life, the universe and human nature :-)

Let me think on that. Maybe some quotes from Vito Corleone on the nature of man will make you cheerier [G]

To Jim:

Re "mutation can change a gene/trait that is already there but can't create a new gene/new trait"

Here is where I see that idea going (fast). There are lots of places I see a new gene or a new trait. Sticking to the horse example, zebras have genes that differ from those in horses. (Actually all people don't have the same genes. Usually the differences are small. I can smell that substance over there, but you can't because you lack the chemical receptor for it, for example. But there are new genes appearing all the time. And not just in bacteria.)

So Jim and I will sit there watching bacteria mutate. We will see _lots_ of mutation.

Sidebar on "lots"
Your genome is so large (so many base-pairs) that it is not possible to copy the genome without statistical error. No two of your cells have the same DNA sequence. Errors creep in. And the genome isn't (as I bet you think it is) a continuous fixed string of bases in a set sequence. The DNA can migrate. Loops and bits of DNA can go in and out all by itself and chunks of DNA do that even more so with the help of the viruses that are in all of your cells (in other words this chunk of DNA can loop on itself, pinch off from the string leaving the string intact, and either float away or insert itself in some other part of the string in that or some other cell). You pull this sequence out from here, stick it there in the middle of that other sequence and voila! you have an entirely new result when you read that section of the DNA strand.
End of Sidebar

So Jim and I are watching all these changes. Most of them don't do much (the DNA and the code are resiliant enough that most changes in the DNA don't cause a change in the gene products, or not much). And for most of these Jim and I both say "that was a normal biochemical event."

Then an event occurs that (finally) is the thing that pushes the DNA across the boundary where it is making something new (a new enzyme say) and Jim will say "That event right there, God 'urged' that reaction to come out just right."

There is no answer to that. To reduce that even further, Jim and I can look at a stream of random numbers, writing them down and assembling genes like stringing beads by choosing the DNA base from the number that came up. Then Jim says "that number right there, the 4366th number was _not_ random even though the numbers preceding and following it were random."

How can you ever test that? There is no refutation of it, but it "isn't fruitful" as I discussed in the post just above this to Khobrah.

Perhaps my reply was misunderstood. In reply to Q's central argument:

""The only real controversy is whether or not random mutation and natural selection simply reinforce and eliminate traits that are already in the genome or if they create new information.""

If I understand you right, when we apply this test to the staph bacterium which we've bred to become vanc resistant, evolution has not occured because the trait was already in the genome like a little homonunculus?

Likewise, if we bred and domesticated wolves over dozen thousand years, selecting for loyalty and obedience, the resulting species would be but expressions of pre-existing canine homonunculii? (homonunculae?)

J

To Jim:

Sorry, I am writing a lot of this quickly while doing other things (Christmas shopping on line at the moment).

Yes, I see. You are quoting Q, and asking for clarification from him on his position (did I get it right finally?)

As I see that argument (that there is a difference between mutation altering a pre-existing trait/gene and mutation creating a new trait/gene) my answer is still as before. One _can_ hold that postition, obviously, but I don't.

I don't see the difference between the two (between Major and Minor Evolution). The statement "that made a new gene" is pretty arbitrary.

So a mutation occurs and makes a change in the DNA sequence (include in "change" not just one base for another but amplifications that add length to the DNA strand). But you can't make any gene product from that changed area (there isn't a start or stop in the sequence). Then you get another change, then another. Then you can make a polypeptide but it doesn't catalyze any reaction (you make a protein, but it is non functional). Then the protein finally is either structural and used in part of the cell or catalyzes some reaction. Where in that did the gene start to exist? Sort of definitional to me.

Nor do I see any way to test the hypothesis. Because it does not say "Major Evolution doesn't exist," but it invokes an untestable mechanism (a "miracle" in the sense of direct intervention by God) when Major Evolution does occur.

And regarding homonunculii/homonunculae. Yes, nice point. We don't want to be sexist here [G]

To Khobrah:

"There is no record of prehistoric bacteria is there?"

Are you asking if there is evidence in the fossil record of bacteria? Yes. Those fossils are called "stromatoliths."

Here are URLs I found in a first pass search:

http://pcb4674-00.su01.fsu.edu/HL1.htm

http://www.markarkleiman.com/archives/000004.html

http://www.biologie.uni-hamburg.de/b-online/library/webb/BOT311/Cyanobacteria/Cyanobacteria.htm

The Cyanobacteria, by the way, were among the first life. The earth had a reducing atmosphere then (N2 and CO2 from volcanoes, mostly, but virtually no oxygen).

There as a whole range of life that lived in that reducing atmosphere. Then some of the life started photosynthesizing, and created "an industrial pollutant", oxygen, flooded the atmosphere with O2 and all that first-tier life was poisoned and died.

I presume the earliest bacteria had some sort of Kyoto Treaty to attempt to stop oxygen production. But the plants wouldn't sign the treaty.

To Q:

When we reach 50 posts in the thread do you buy us a pizza?

What about when we reach 100 posts?

To all debating parties,

The comments on this post cover much ground and I've been out-of-pocket for a few days. I just cut and pasted everything to MS Word to read it, and it made up 50 pages… This is a bit awkward to manage and may intimidate some new folks from chiming in. So let me try to capture the many threads so far before I even attempt to jump back in.

1. How scientific are fields that study things than they cannot replicate? I personally agree with much of what Luke was saying and will discuss this soon.

2. Timing: The age of the earth and the age of the universe.

3. How new species develop. There are several threads in here (micro vs. macro evolution, timing of new species (all at once vs. continuous), how new species might develop (Darwin was way off base here, but that was partly due to ignorance about cells). BTW, I completely disagree with Drew and Khobrah's assumption that ALL life evolved from a BACTERIA. Jim also asked me some questions that I will answer as part of this thread.

4. Theory-driven science vs. data-driven science (Drew's perspective on this particularly intrigues me. He claims that theory-driven science is superior, but likes to promote Gould. I have read several of Gould's books and Gould was very data driven).

5. The original point of the post discussing the eventual death of Darwin's theory and the relevance of Kuhn.

Any others? Once we agree to the various threads, I propose starting that many new posts. This should make it easier to for us (and others) to follow and join in. The only downside is that Drew won't get to see what happens when we hit 100 comments on one post. Unless he takes this as a challenge which it is not ;-)

While expectantly awaiting Q's comments on the points he just outlined, he used another set of terms I have never heard before.

I only know one scientifice method. What is this theory-driven/data-driven difference?

I am going to try to post something sort of complicated. This may look like garbage on your screen.

I have been trying to avoid much biochemistry here, but Khobrah's question ("Why do I think bacteria and humans have a common ancestor") and my statement to Q ("I don't see any difference between macro and micro evolution) both will require a little knowledge of the genetic code and protein synthesis so here is a primer on the genetic code:

If this _doesn't_ format for you, look at:

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

The Genetic Code

The Genetic Code
Index to this page

• The RNA Codons
• The DNA Codons
• Exceptions to the Code

The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.

One codon, AUG serves two related functions:

• it signals the start of translation
  
• it codes for the incorporation of the amino acid methionine (Met) into the growing polypeptide chain
  

The genetic code can be expressed as either RNA codons or DNA codons. RNA codons occur in messenger RNA (mRNA) and are the codons that are actually "read" during the synthesis of polypeptides (the process called translation). But each mRNA molecule acquires its sequence of nucleotides by transcription from the corresponding gene. Because DNA sequencing has become so rapid and because most genes are now being discovered at the level of DNA before they are discovered as mRNA or as a protein product, it is extremely useful to have a table of codons expressed as DNA. So here are both.

Note that for each table, the left-hand column gives the first nucleotide of the codon, the 4 middle columns give the second nucleotide, and the last column gives the third nucleotide.

The RNA Codons

Second nucleotide

UCAG

U
UUU Phenylalanine (Phe)UCU Serine (Ser)UAU Tyrosine (Tyr)UGU Cysteine (Cys)U

UUC PheUCC SerUAC TyrUGC CysC

UUA Leucine (Leu)UCA Ser UAA STOPUGA STOPA

UUG LeuUCG Ser UAG STOPUGG Tryptophan (Trp)G
C
CUU Leucine (Leu)CCU Proline (Pro)CAU Histidine (His) CGU Arginine (Arg)U

CUC LeuCCC ProCAC HisCGC Arg C

CUA LeuCCA ProCAA Glutamine (Gln)CGA Arg A

CUG LeuCCG ProCAG GlnCGG Arg G

A
AUU Isoleucine (Ile)ACU Threonine (Thr)AAU Asparagine (Asn)AGU Serine (Ser)U

AUC IleACC ThrAAC AsnAGC Ser C

AUA IleACA Thr AAA Lysine (Lys)AGA Arginine (Arg)A

AUG Methionine (Met) or STARTACG ThrAAG LysAGG Arg G

G
GUU Valine ValGCU Alanine (Ala)GAU Aspartic acid (Asp)GGU Glycine (Gly)U

GUC (Val)GCC AlaGAC AspGGC GlyC

GUA ValGCA AlaGAA Glutamic acid (Glu)GGA GlyA

GUG ValGCG AlaGAG GluGGG GlyG

The DNA Codons

These are the codons as they are read on the sense (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the antisense strand of DNA (3' to 5') as the template. [Discussion]

This table could well be called the Rosetta Stone of life.

The Genetic Code (DNA)

TTTPheTCTSerTATTyrTGTCys

TTCPheTCCSerTACTyrTGCCys

TTALeuTCASerTAASTOPTGASTOP

TTGLeuTCGSerTAGSTOPTGGTrp

CTTLeuCCTProCATHisCGTArg

CTCLeuCCCProCACHisCGCArg

CTALeuCCAProCAAGlnCGAArg

CTGLeuCCGProCAGGlnCGGArg

ATTIleACTThrAATAsnAGTSer

ATCIleACCThrAACAsnAGCSer

ATAIleACAThrAAALysAGAArg

ATGMet*ACGThrAAGLysAGGArg

GTTValGCTAlaGATAspGGTGly

GTCValGCCAlaGACAspGGCGly

GTAValGCAAlaGAAGluGGAGly

GTGValGCGAlaGAGGluGGGGly

*When within gene; at beginning of gene, ATG signals start of translation.

Exceptions to the Code

The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms. However, some exceptions have been found. Most of these involve assigning one or two of the three STOP codons to an amino acid instead.

Mitochondrial genes

When mitochondrial mRNA from animals or microorganisms (but not from plants) is placed in a test tube with the cytosolic protein-synthesizing machinery (amino acids, enzymes, tRNAs, ribosomes) it fails to be translated into a protein.

The reason: these mitochondria use UGA to encode tryptophan (Trp) rather than as a chain terminator. When translated by cytosolic machinery, synthesis stops where Trp should have been inserted.

In addition, most

• animal mitochondria use AUA for methionine not isoleucine and
  
• all vertebrate mitochondria use AGA and AGG as chain terminators.
  
• Yeast mitochondria assign all codons beginning with CU to threonine instead of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).
  

Nuclear genes
Violations of the universal code are far rarer for nuclear genes.

A few unicellular eukaryotes have been found that use one or two (of their three) STOP codons for amino acids instead.

The vast majority of proteins are assembled from the 20 amino acids listed above even though some of these may be chemically altered, e.g. by phosphorylation, at a later time.

• selenocysteine. This amino acid is encoded by UGA. UGA is still used as a chain terminator, but the translation machinery is able to discriminate when a UGA codon should be used for selenocysteine rather than STOP. This codon usage has been found in certain Archaea, eubacteria, and animals (humans synthesize 25 different proteins containing selenium).
  
• pyrrolysine. In one gene found in a member of the Archaea, this amino acid is encoded by UAG. How the translation machinery knows when it encounters UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet known.
  

Welcome&Next Search

6 June 2003

That may have been only semi-successful but you have a URL to the original web site.

There are two kinds of nucleic acids - DNA and RNA. Both are long chain polymers (subcomponent molecules strung together in a long chain). They differ in what makes the "string" that connects the subcomponents, and there is a small difference between the two in the subcomponents, but that isn't too important to this (so far anyhow).

This long chain can be thought of as a string of letters. The alphabet is only U,G,A, or C (for RNA) or T,G,A or C (for DNA). So you can read along the chain:

UAAGCAGGCAUUAUGCAUC.......

This chain can be translated into a protein. A protein is a polymer (long chain of repeating units drawn from the subcomponent bag) too. The code describe above is how you read the instructions in the RNA molecule to make a protein.

The RNA is read in sets of 3 bases at a time. For example if the next 3 bases are GUU you add a Valine amino acid at the next bead in the growing protein chain. If the one after that is CCU you add a proline next. Get it? If not, raise your hand because this will be the basis for lots more later.

The sets of 3 bases are called "codons". You will note there is a start codon "AUG" That tells the thing that reads the RNA and which assembles the protein per the encoded instruction "Start here". And there is a stop codon. Actually there are several stop codons. (The code allows for 64 3-letter codons but there aren't that many amino acids commonly used so some of the codes are "redundant" (the real term is "degenerate" - they call for the same amino acid as some other codon.

The Stop codon tells the thing that is making the protein (a Ribosome) to stop making that protein, let the RNA and the new protein both float away, and then the Ribosome floats around looking for another RNA molecule to read.

The ribosome always reads in one direction down the RNA, always starts at AUG, assembles whatever the string says to assemble, and quits at STOP.

The programmers among you can think of STOP (for example the UAA codon, one of the stop codons, as EOL in the computer language Basic.

The cell can copy it's DNA (to make more cells), make RNA from the DNA gene, and make proteins from the RNA.

I am going to stop here and wait for everyone to catch their breath and ask questions.

There are some major implications to what I just said, some obvious and some not obvious.

Now I am going to say, in response to Khobrah, why I think me and the E.Coli bacterium growing on your snack counter once had a common ancestor.

Both ‘E’ (the bacterium) and I use DNA for our genome and RNA as an intermediate step for translating the genome into proteins. (We use proteins in part for our structure, but in large part as the enzymes that run all of our chemistry). There are lots of other long chain repetitive molecules each of us might use, but we use the same ones.

E and I both happen to use proteins to run all of our biochemistry. (Proteins are long chains of amino acids). There are other long chain molecules we could use as enzymes, but we both choose chains made of amino acids.

There are lots of amino acids. We don’t use all of them (we use less than half). E and I both chose the same ones to use and the same ones to eschew.

E and I both use GCA and T for the bases to encode the data in our DNA and GCA and U to encode the data in our RNA. There are lots of other bases. But we both use the same ones.

You could read the RNA in either direction (5’ to 3’ or 3’ to 5’). But we both read in the same direction.

I can’t quantitate any of those. For example I can’t tell you how many other long chain molecules life might use instead of DNA, to encode genetic data, (there are lots) so I can’t calculate a probability of me and E both choosing DNA by chance.

But there is the code: 64 permutations (64 different codons) and we all use the same ones. That I can quantitate (probably incorrectly but Khobrah will correct me. He always does). What are the odds that all 64 codons would match? Given that there are 22 amino acids (counting Start and Stop as equivalent output). Not counting the degeneracy (which matches) does that mean the odds of that happening randomly are 1/22^64 ("One over Twenty-two to the sixty-fourth power")? The degeneracy thing has to be accounted for, but E and I chose the same codons to make redundant. Anyhow Khobrah can tell us the number just for the odds of having the same coding. It is “really small”.

So I don’t buy E and I just happening to choose to use all the same codons for all the same amino – acids and “punctuation marks” (Start and Stop).

You can say that one common ancestor hit on that encoding, and that E and I both inherited it. You could also say that God chose to give me the same coding (after 3 billion years) he gave to E coli. But that is the prankster God I don’t believe in (why would he do that? If he is trying to fool us, He can so why bother?)

I don’t buy that bacterial life arose when the earth was 500 million years old and we just happened randomly to make all the same choices when multicellular life came on the scene about 2.5-3 billion years later.

Major and Minor Evolution

As I said, I had never heard the phrases “Major Evolution” and “Minor Evolution” before. And I can’t imagine how there could be any such difference. Now I can explain why I think that.

As I understand this concept, mutation can change an already existing inheritable trait, but can’t create a new inheritable trait. Is that right?

First, I think “trait” and “gene product” are the same thing. That’s what an inheritable trait is at the molecular level. Let’s go back to that doctor thinking about the bacteria that might become resistant to an antibiotic. Let’s assume the antibiotic is Penicillin.

Penicillin is a chemical that kills bacteria. Penicillinase is an enzyme (a protein, a gene product made according to the template codons in a gene) that cleaves penicillin into two innocuous subunits. If a bacteria has the gene for penicillinase it can make penicillinase, can metabolize penicillin into harmless byproducts, and is resistant to penicillin. That’s what I mean by a trait being a gene/gene product. (The trait may involve more than one gene, but that doesn’t change what I am going to say.)

As I understand the Major/Minor evolution idea it says a gene can mutate a bit, changing the already existing gene but can’t create a new gene. It could modify the gene the bacterium already has so that gene, instead of doing whatever it did before (cleaving some other chemical. A sugar in the environment, maybe) or makes it active instead of inactive. But making a whole new gene is somehow qualitatively different from modifying a gene you already have.

Is that about right?

Lets look at that table with the genetic code.

A bacteria has lots of DNA. A lot of that DNA makes RNA that is used as a template to make proteins. A lot is not. From memory about 60% of the DNA in a bacteria is in structural genes (genes that make proteins). The rest is not. In an animal cell only about 1% is in structural genes.

What is all the rest of that DNA doing? Well, some is regulatory DNA. Some of the DNA is a switching mechanism that can turn a whole bank of genes off and on. Metabolizing some certain carbohydrate may require 6 genes. So you have a regulatory gene that turns all 6 off or on at once, depending on whether that carbohydrate is around at the moment.

Some probably does nothing at all. Crabs, as I recall, have enormous long runs of “AAAAAAAAAAA…..” going for thousands of bases. That would code for “Lysine- Lysine- Lysine- Lysine- Lysine-….” but crabs don’t make such a poypeptide. It is apparently “just there.” If you think about it, that long run of A’s is the minimalist form of a parasite, carried along from generation to generation every time the crab’s cells divide (there are other parasitic viruses living in your cells. Sometimes they migrate out of the DNA and become free viruses but they can just sit in the cell’s DNA for hundreds of generations).

Now lets look at one triplet of bases in this bacteria’s DNA. Let’s pick this triplet here that reads:

UCG That codes for Serine

These bases can mutate for any of a variety of reasons. Background radiation, metabolites in the environment. Just by quantum indeterminancy.

So this triplet might, in one bacteria of the billions of billions in the culture dish (or patient) have the U mutate to G

GCG That codes for Alanine

Or the U mutate to A

ACG That codes for Threonine

All those are minor evolution as I understand it.

Lets look somewhere else in that bacteria’s genome.

Here is another G, but it is followed by U and G not by C and G

UUG that codes for Leucine

If the initial U changes to a G that becomes

GUG which codes for Valine

If the initial U changes to A that becomes

AUG and that codes for Start!

By creating a new start codon you now have created a sequence of DNA that will be read by those ribosomes until the ribosome comes to a stop (one that was already there, perhaps in the next gene down or one that arose by mutation as well.

This new start codon means you now have a new gene product.

So G changing to U or G is minor evolution, and G changing to A is also minor evolution unless the two bases following the G are U and G in that order. In that last case it was Major Evolution and required the direct intervention of God.

One can believe that God “watches over every sparrow and holds him up” and one can also believe that God “watches over every G base that is followed by a U and a G insuring that it only mutates to C or U, not A” but I don’t believe that.

I believe the same rules of chemistry apply to that G regardless of which two bases follow it.

I don't believe this (at all) but thought this crowd might find it amusing.

http://www.nwherald.com/StyleSection/305208887246087.php

This clown (er, scientist) says there is a gene that determines if you believe in God or not (and he has identified the gene). This is the same guy who discovered the gay gene a while back.

Hmm, I could argue that "Catholic/Mormon" religious belief makes you have lots of children so there are more children with your Catholic (or Mormon) gene in the next generation.

(No, I am not serious but the guy in the article is serious)

Thinking about this some more, I have tried to take money out of the picture. (When I get stumped by an economic question I find it helps to eliminate the concept of money and think only of the flow of goods and services).

Consider an economic universe with only two people in it, Drew and Khobrah. Both produce goods and services and both consume goods and services.

Drew wants to consume more goods and services than he produces. The only way he can do this is if Khobrah (the only other person in that universe) produces goods and services, consumes less than he produces (ie Khobrah saves) and then Khobrah lends the unconsumed goods and services to Drew. Since Khobrah is a member of the species Rational Economic Man (Homo Economicus Rationalis), Khobrah is willing to do this (loan stuff) only because he expects to be repaid at some future time when Khobrah will choose to consume more than he produces.

So Drew can consume more than he produces, but only for a time. Eventually Khobrah has to consume more than Khobrah produces and Drew consume less than Drew produces.

(This doesn't mean that Drew ever has to consume fewer goods and services than he is currently consuming. For example Drew could even consume 25% more tomorrow than he is consuming today if he produces 50% more than he is producing today, and ships the surplus to Khobrah.

Now replace "Drew" with "Everybody in the US" and "Khobrah" with "Everybody in China". All that still holds true. All the people in the US can consume more than they produce (for a while) because all the people in China are producing more than the Chinese are consuming, and loaning the excess to the US. But eventually the current accounts deficit has to correct.

Now replace "Drew" with "All the people in Nevada" and "Khobrah" with "All the people in Wyoming". Doesn't it still hold true? All the residents of Nevada, singly or as a group, can't consume more than they produce indefinitely. So why doesn't Nevada run a current accounts deficit with Wyoming and Wyoming a Current Accounts surplus?

Is it because in the case of states (not countries) Drew and Khobrah have an uncle, Sam, who quietly taxes both of them and shifts that tax money around without either of them noticing, so the current accounts deficit is corrected? I can't see it being because Wyoming and Nevada have the same currency, bond market and central bank. If Drew and Khobrah as individuals use the same monetary units and same bank, Drew still can't consume more than he produces indefinitely.

The Quantum view (a collection of individuals) and the Classical view (US States as entities) seem to give different answers. Anybody see how US states (or any other collection of individuals that are _not_ a country) correct production/consumption imbalances?

If you simplify things to the point where we are just talking about shirts and oranges, there are no differences between intrastate commerce and intracountry commerce. Currency exchange and the role of government intervention (e.g,. Taxing Khobrah and subsidizing Drew) do have an impact, but for the sake of discussion let's ignore these. You can have countries with a common currency (e.g., Euroland) and while a tax-free government is a stretch, we can imagine two governments with similar taxation schemes that do not impact trade).

However, while I do not see a necessary difference between intrastate and intracountry trade (one of your main issues), I do have a problem with oversimplifying the model to just Drew and Khobrah. This makes trading a zero-sum game where trade deficits always have long-term implications.

Now I don't believe this is true in the real world. Let's create a slightly more complex model. Assume country La Mancha with two states (Drewtopia and Khobrahstan) and country LowWagesRUs. La Mancha is very productive. The innovative Drewtopians and Khobrahstanis are constantly trading amongst themselves and creating new products that create new wealth for their citizens. With some of their ever increasing wealth, they also buy items from LowWagesRUs.

The citizens of LowWagesRUs do not buy much from La Manchans since they prefer to use the profits from their trading surplus to develop their country. Some La Manchan's are concerned about running a trade deficit with LowWagesRUs. However, all international purchases accounts for about 10% of La Manchan spending. Is this a problem?

My perspective, which may not be shared by economists, is that this is perfectly fine so long as the La Manchan economy wealth continues to grow (or even stays the same). It only becomes a problem, when La Manchans start importing so much that they lose wealth in doing so.

Real life economics is not a zero-sum game. So if new wealth is being created, it needs to be considered in all discussions about trade.

Yes, I know the example was simple. And there are ways out if you have different currencies (you can devalue or have a different rate of inflation than the other guy).

And yes, the absolute dollar (or utile) value of the trade deficit is not a problem as long as the size (and debt service) are manageable given your overall size.

But I am still bothered that Interstate and International current accounts deficits don't seem entirely the same.

Perhaps I misunderstood your question. Let me try another tact (and if that doesn't work, please elaborate your question).

Ignoring models altogether (and still ignoring the role of government) there are two big differences between interstate trade and international trade. The currency exchange, as you mentioned, is a large issue. Countries like China deliberately peg their currency to be worth much less than the dollar to help their exports. Other currencies (such as the Euro) will gain or lose value against the dollar and may be used as balancing issues.

Another issue is how country A pays for the trade imbalance. In my opinion, this is one of the more important factors in the discussion. If country A goes into debt to pay for the goods from country B, then this is bad for country A over the long-term. If the debt grows large enough (both in absolute terms and/or as a percentage of country A's wealth), then it will adversely impact the value of country A's currency relative to adjustable currencies (e.g., the dollar will drop against the euro, but not against the Chinese yuan).

Now, absent the currency issue, this situation might be going on with interstate trade (e.g., Californians may be buying goods from Vermont on credit and plan on paying for them with the appreciation of their real estate). However, no one seems to think interstate commerce is a bad idea, even if some states have imbalances (as they must unless you think all states perfectly average out). This is why I think the issue that should be cause for concern is not who you trade with, but how you pay for your purchases (cash vs. financing). (Caveat – the other big difference is the one I was trying to ignore for simplicity's sake. The Federal government does redistribute wealth from some parts of the US to other parts of the US and this may serve to compensate for some trading imbalances).

So due to the US current accounts deficit the Chinese now have a bunch of US
Dollars. They can a) spend those (buy stuff from us with dollars or buy
stuff from somebody else, say buy oil from the Saudi's with dollars). If
they buy stuff from the Saudis that basically doesn't change anything
(right?). The dollars are still out there, held by someone not inside the
"membrane" of the US (I think of trade in terms of flux across a
semipermeable membrane). Those outside-the-membrane dollars can go back
inside the membrane if the Chinese or Saudis buy stuff _from somebody inside
the membrane. That is a current accounts surplus and everything is now back
to zero net current account surplus/deficit.

If they don't buy anything from somebody inside the US they can hold the
dollars in a strongbox. They can turn the dollars into US Treasuries (which
does nothing, right? Those turn back into dollars-outside-the-membrane when
the Treasuries are eventually cashed in.)

Hmm, "So what" I can hear you say. Is that the answer? If the Chinese hold
US dollars that is their business. There is a potential effect on the US
Bond Market lurking in there. If the Chinese have lots of US Treasuries they
can suddenly not be interested in rolling them over any more, but that is
true of any other holder of US treasuries. The likelihood of the Chinese
losing interest in US Treasuries is a little different than the likelihood
of me, say losing interest. The Chinese are assuming a currency exchange
risk by holding US dollars but I am not. So they are more likely to lose
interest some future day.

Is the answer (to the little question of whether a current accounts deficit
ever has to come back to zero at some future date) "not necessarily because
the guy holding the dollars might choose to do that ad infinitum"?

(The original question of whether a US State or county can have a current
accounts deficit we can deal with in a bit. I just thought of someone else
to ask)

I'm starting to better understand your point. I think part of the confusion is that we are talking about two different issues: trade deficits and oversea dollars. To add to the confusion, these issues may impact each other.

I do not believe trade imbalance is a major issue. If we bought the Chinese goods with gold (so currency and debt issues never arise), there would be no problem so long as we were still producing or otherwise obtaining enough wealth that our stockpiles of gold continued to grow. Agreed?

I now believe your main concern is the issue about having massive amounts of dollars overseas (and the related issue of owing foreigners massive amounts of debt). Let me know if this is correct before I spend time on this.