A Revolution in Evolution Is Underway

Thomas More Lawcenter ^ | Tue, Jan 18, 2005

[Jay777]

ANN ARBOR, MI — The small town of Dover, Pennsylvania today became the first school district in the nation to officially inform students of the theory of Intelligent Design, as an alternative to Darwin’s theory of Evolution. In what has been called a “measured step”, ninth grade biology students in the Dover Area School District were read a four-paragraph statement Tuesday morning explaining that Darwin’s theory is not a fact and continues to be tested. The statement continued, “Intelligent Design is an explanation of the origin of life that differs from Darwin’s view.” Since the late 1950s advances in biochemistry and microbiology, information that Darwin did not have in the 1850s, have revealed that the machine like complexity of living cells - the fundamental unit of life- possessing the ability to store, edit, and transmit and use information to regulate biological systems, suggests the theory of intelligent design as the best explanation for the origin of life and living cells.

Richard Thompson, President and Chief Counsel of the Thomas More Law Center, a national public interest law firm representing the school district against an ACLU lawsuit, commented, “Biology students in this small town received perhaps the most balanced science education regarding Darwin’s theory of evolution than any other public school student in the nation. This is not a case of science versus religion, but science versus science, with credible scientists now determining that based upon scientific data, the theory of evolution cannot explain the complexity of living cells.”

“It is ironic that the ACLU after having worked so hard to prevent the suppression of Darwin’s theory in the Scopes trial, is now doing everything it can to suppress any effort to challenge it,” continued Thompson.

[Ichneumon]

For a good example of trying to "quantize a continuum", see this page on the comparison of various fossil hominid skulls. Scroll down a page or two to the table, "Creationist Classifications of Hominid Fossils". As the chart makes entirely clear, and the text explicitly points out, when the creationists try to "quantize" fossil skulls into the two disjoint categories of either "ape skull" or "human skull", they trip all over themselves (and each other) trying to decide which one goes where.

Excerpt:

As this table shows, although creationists are adamant that none of these are transitional and all are either apes or humans, they are not able to tell which are which. In fact, there are a number of creationists who have changed their opinion on some fossils. They do not even appear to be converging towards a consistent opinion. [...] Creationists, on the other hand, assert that apes and humans are separated by a wide gap. If this is true, deciding on which side of that gap individual fossils lie should be trivially easy. Clearly, that is not the case.

[highligting in original] The point is that even if one refuses to accept the evolutionary explanation for the apparently transitional skulls between ape and man, the fact remains that the skulls actually *do* map out a *continuum*, with various skulls having more/less ape and less/more human features, and it is an error which leads to immediate confusion if one attempts to "force" the skulls into artificially quantized categories of "all ape" or "all human".

The *reality* of the skulls is that they lie along a spectrum from "fully ape" on one end and "fully human" on the other, with "some of both in varying amounts" in between. Any attempt to quantize them into separate "buckets" immediately ties itself in knots and fails, as the chart makes quite clear.

[Ichneumon]

There are things that are so intricate that it's difficult to see how they could be the result of accidental transition. Carbohydrate metabolism, for instance, or DNA repair.

There has actually been quite a lot of interesting research and progress on both of those issues, but I'm too tired right now to go Googling for it (I've been up all night, about to go to bed now). Suffice to say that although the processes by which they arose are not fully understood yet, there are already plausible precursor systems, and biochemical evidence of the nature of the earlier stages.

And remember, in 1900 it was "difficult to see how" the Sun could produce so much endless energy. I actually read a creationist book from that era which argued that since no known (chemical) process could produce so much energy for thousands of years, it must be proof that God was actively running it. Needless to say, science went on to learn how such natural processes actually work without direct divine intervention to keep them running each day.

For now, here's a previous post of mine concerning research into the evolution of the Krebs metabolic cycle:

What do you have concerning the development of the Krebs cycle?

Ooh, glad you asked, now I have a good excuse to post this cool animation of the Krebs cycle:

To read up on the evolution of the Krebs cycle (also known as the citric acid cycle), a good starting point is:

The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution, Melendez-Hevia E, Waddell TG, Cascante M, J Mol Evol. 1996 Sep;43(3):293-303

A portion of the abstract:

Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.

From the body of the article:

In the evolution of the metabolism, the achievement of the fundamental steps of the Krebs cycle was not difficult at all. Almost all of its structure previously existed for very different purposes (anabolic), and cells had to add just one enzyme (succinyl-CoA synthetase for the transformation of succynol CoA into succinate) to convert a collection of different pathways into the central cyclic pathway of the metabolism. This is one of the most clear cases of opportunism we can find in evolution.

[...]

The Krebs cycle has been frequently quoted as a key problem in the evolution of living cells, hard to explain by Darwin's natural selection: How could natural selection explain the building of a complicated structure in toto, when the intermediate stages have no obvious fitness functionality? This looks, in principle, similar to the eye problem, as in 'What is the use of half an eye?' (see Dawkins 1986, 1994). However, our analysis demonstrates that this case is quite different. The eye evolved because the intermediary stages were also functional as eyes, and, thus the same target of fitness was operating during the complete evolution. In the Krebs cycle problem the intermediary stages were also useful, but for different purposes, and, therefore, its complete design was a very clear case of opportunism. The building of the eye was really a creative process in order to make a new thing specifically, but the Krebs cycle was built through the process that Jacob (1977) called 'evolution by molecular tinkering,' stating that evolution does not produce novelties from scratch: It works on what already exists. The most novel result of our analysis is seeing how, with minimal new material, evolution created the most important pathway of metabolism, achieving the best chemically possible design. In this case, a chemical engineer who was looking for the best design of the process could not have found a better design than the cycle which works in living cells.

Also see (link goes to full text):

A mitochondrial-like aconitase in the bacterium Bacteroides fragilis: Implications for the evolution of the mitochondrial Krebs cycle, Anthony D. Baughn and Michael H. Malamy

While on the subject, I can't resist providing a link to this nifty site I ran across while digging up the above links. It's a multi-page animated tutorial on cellular respiration (including the Kreb's cycle), and it's a great introduction to the whole subject. It also makes fascinating observations like, for example, the fact that our critical dependence upon oxygen, and our lungs, red blood cells, and all related systems, don't actually play any direct role in our cellular metabolism -- they exist solely in order to remove electrons from the mitochondrial electron transport system, a minor (but vital) sideshow in the actual core metabolic processes of the cell. We don't need oxygen for energy or metabolism, as many people presume, we just need it to keep the assembly line clear...

That same website has other cool biology tutorials, hit the "outline" link at the bottom to see an index.

Yet more reconstruction of the evolution of the Kreb's cycle:

The Molecular Anatomy of an Ancient Adaptive Event: Protein engineering identifies the structural basis of a 3.5 billion-year-old adaptation, Antony Dean, American Scientist, Volume: 86 Number: 1 Page: 26 DOI: 10.1511/1998.1.26

In short, the Krebs cycle arose as a relatively minor modification to pre-existing cellular biochemical processes which were being used for amino acid synthesis and early iron-based metabolism.

Since the next question will undoubtedly be, "where did the iron-based metabolism come from", next we will visit:

The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence, Di Giulio M., J Theor Biol. 2003 Apr 7;221(3):425-36

...which is only one of the recent confirmations of this model of the origin of life as we know it:

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells, William Martin and Michael J. Russell, Phil. Trans. R. Soc. Lond. B, DOI 10.1098/rstb.2002.1183

A related observation is:

"The oldest of these proteins was ferredoxin, a biosynthesis enzyme that contains iron-sulfur clusters and that transfers electrons (hydrogen-atom equivalents). This protein he reconstructs as having a negatively-charged tail; this can stick to positively-charged objects like mineral surfaces with their metal ions -- which is consistent with the view of Gunter Wachtershauser that life originated from iron-sulfur-associated chemical reactions on mineral surfaces, and that the Krebs Cycle dates from this time. Note that the Krebs Cycle's members are all acids -- negatively-charged ions -- meaning that they can stick to mineral surfaces."
-- from this webforum discussion

In short, life most likely originated in iron monosulphide pockets around hydrothermal ocean vents.

Finally, since someone is bound to mention the creationists' favorite biochemist Behe, it seems appropriate here to point out one of Behe's many whoppers. In his book "Darwin's Black Box", he wrote:

"There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems."
[...]
"In effect, the theory of Darwinian molecular evolution has not published, and so it should perish"

What planet is *he* living on? There have been countless statements by biochemists expressing their bafflement at how Behe could make such a transparently false claim.

One web author points out that a simple MEDLINE search turns up *thousands* of such papers -- so what's Behe's excuse? But my main reason for bringing up this particular web page is that it's a really decent compilation of links to papers on various aspects of molecular evolution, and a good starting point for finding answers to the kind of question you pose. That page is Behe's empty box: alive and published -- Some published works on biochemical evolution.

[PatrickHenry]

I agree entirely with Ichneumon's post. I also agree with what Physicist said -- that there most certainly are what we may regard as quanta at the level of individuals (or their fossils). The continuum of common descent is from one generation of individuals to the next. I think that in all my discussions I was using "species" as the potentially erroneous category of quantization.

[Doctor Stochastic]

Excellent. What I was going to post would have been redundant pleonasm, not to mention superfluously excess.

I would like to add a reference to Luisi's paper: About various definitions of life. (The link is to a .pdf in a journal.) There's also a new book by Robert A. Freitas, Kinematic Self-Replicating Machines, which addresses definitions of life with a lot of discussion about the difference between reproduction and replication.

[discostu]

The data is digital, it's 1s and 0s, that's digital. And most software types never worry about data storage, that's under the hood stuff for hardware driver developers. In the world of software if you don't learn anything about under the hood until you take classes that are on under the hood stuff, it's a black box until then, something you don't have to worry about how it works just understand the API calls to put stuff there and get it back. And there's nothing wrong with black boxing stuff too complicated for the level of the student.

[discostu]

No I'm refering to science done with too small a sample set, which is how most science starts. It's a natural by-product of science. Big science requires even bigger sample sets, larger than one person could possibly collect in their lifetime, but big science always starts with the work of one person. They do what they can, publish their findings and start us on a new road.

I have no theory as to the cause, I don't have the background necessary to form a theory that would even be as good as Darwins. But I can see in the fossil record that it happens, and it must have a cause, my own lack of ability to theorize a cause doesn't mean it does happen.

[atlaw]

Oh, I see. Had I used the (inaccurate) term sound byte, you would have understood my point, and supplied something resembling a cogent response. Wordsmithing (especially incompetent wordsmithing) generally indicates an interest only in obfuscation (confirmed by the balance of your posts).

[discostu]

No it doesn't have to. Science isn't about efficiency, science is about knowledge and if something can't be explained with simple efficient math then that's just how it is. Ever actually looked at the math to figure out how much load a building can take? It's a bitch, before electronic computers it could take structural engineers and professional mathmeticians (human computers, no really "computer" was the job title, it's where the item got its name, from the first people to lose their job because of it) months to work it out. Nothing simple about it.

No the faith can't. Human language isn't up to the task.

Global warming would be an excellent thing to study in school, for the opposite of the same reasons. Global warming is something most laymen agree exists, and yet every scientific model has failed utterly, none of the data says any warming is happening, and the bulk of the scientific community is in the process of throwing it out. In global warming they're trying to fit the data to a model and failing miserably meanwhile the data shows the base concept is fiction, in evolution they're fitting modelss to data and keep getting more data that show the base concept is correct it's just how we try to work it that's having problems. Both are excellent ways of teaching the scientific method, one shows how the method progresses knowledge and the other shows how the method disgards bad ideas. Also if we taught global warming in schools we'd help take acceptance of it out of the laymen community.

[discostu]

Orbiting electrons are what we learned in the 80s. Schooling took a giant leap backwards in the 70s, actually it probably started in the 60s with the invention of new math, pretty much all the dumb stuff that goes on in schools today evolves from that same mentality "it's not important that they get it right, it's important they understand it" with no explanation of how people that don't get it right could possibly understand it. Then things took another leap backwards in the 90s with outcome based education (forget understanding it, just make sure they feel good). The nation's educational system is devolving.

[MineralMan]

Well, maybe my school back in the 60's was better than most, but I learned a heckuva lot there. I think I was taught the Bohr model back in grammar school, but by high school, we were way beyond that in Physics and Chemistry classes. Never mind that the models have changed further since then. Maybe I just had good teachers.

[discostu]

Some of it's intuitive, kids can usually move in the right direction towards catching the ball right from the start, kids have a hard time grasping their own speed so they need to learn how fast to run to be in the right place at the right time, but they'll be aiming in the right direction fromthe start. There's a lot of that stuff humans just get, like bracing a large door (like on a barn), have non-construction people put a big wooden door on something and when they see it wobbling they'll immediately use more wood to put a big X on the door bracing it, which happens to be the exactly right thing to do. We've got some pretty cool stuff in the back of our brains.

[discostu]

Your school in the 60s was better than mine in the 80s, which in turn was better than what we're putting kids through now. Good teachers help, but remember the model is how teachers are taught to teach. It took new math a while to phase in because when hey first came up with it none of the teachers had learned it so that's not how they taught, but eventually all of the teachers had learned that's how you're supposed to teach, and shortly after that the high school of our nation lowered the math requirements necessary for a degree.

[WildTurkey]

The data is digital, it's 1s and 0s, that's digital.

The stored data is NOT 1's and 0's. You must have the proper circuits to analyse the voltage patters and extract the data from the disk.

[discostu]

Which is all under the hood crap nobody cares about and isn't taught until you take classes that focus under the hood. See that's the difference between what high school does and college. In college if they decide something is too complicated for this level they put it in a black box and tell you not to worry about, they tell you how to figure out the out put and if you really want to know what goes on inside the box take this other class. In high school if they decide something is too complicated for this level they make up a simple version that'll give the same output but isn't what's really going on. The college method is better because it doesn't give the student something to unlearn if they progress in that field. The high school method is stupid because it wastes time BSing the student, then if htey progress in that field more time gets wasted to unlearn the BS.

[js1138]

And most software types never worry about data storage...

This is unrelated to the discussion, but back about 1982 I has a Trash-80 computer that used cassette tape for storage. It was incredibly slow, and several people wrote alternate storage routines. I typed in one such assembly language routine from a magazine and wound up debugging it, due to a typo.

This was an interesting process. The tape signal was noisy, and the program had to filter the raw signal.

AS a result of this I have enormous respect for the folks who have packed hundreds of gigabytes into cheap disk drives.

[PeterFinn]

"Just thought I should correct your typo."

No typo. Read it again and check your grammar and do use a dictionary instead of MS Spell Check.

And (checking my pings) your still the only person to include himself in the group of Psychotically enraged Darwinist-atheist-antiChristians by taking offense at the comment.

By default, no one else on this thread has accepted the label and I do not levy it at them.

Just you.

Nyah-nyah-nyah-nyah-nyah!

[general_re]

I had one of those. It was just enormously cool to ditch the cassette in favor of my single-sided, single density 5-1/4" floppy drive. 90 KB of random access storage per disk - woohoo! ;)

[Alamo-Girl]

Thank y’all so much for your replies!!!

PatrickHenry: I think we have different understandings about what this fallacy is all about. To me, the fallacy of quantizing the continuum occurs when: (1) the subect being dealt with actually is a continuum; and (2) someone siezes upon an artifically defined segment thereof (a quantum) to declare something about that segment which is allegedly unique to it and not to that segment's boundry regions.

We agree on what the fallacy is about up to the point about the assertion of a “segment’s boundary regions”. To use Ichneumon’s rainbow – the fallacy would also say that one cannot distinguish red from blue even though they do not sit in juxtaposition – because one would have to base that determination on a quantization of red and blue. All one could say is blueness>redness in the continuum of the rainbow.

The application to biology is readily apparent. If Darwin were right, and all life is related by common descent, then it form a continuum, rather than a collection of discrete groupings we call "species." Thus, even where no intermediate forms are now alive, the theory predicts that they once did live, and perhaps will be found.

Indeed. Darwin’s theory is that the continuum exists. And certainly, the geologic record is a continuum but Darwin was speaking to the continuum of life.

Further, Darwin’s theory also asserts that there is an ancestry in the continuum leading from species to species and that is what I am saying requires a quantization of the continuum to assert. To use the rainbow metaphor again, it would be saying that because of the juxtaposition in the continuum of the rainbow, blueness descended from greenness which descended from redness (which we know is not a heritable trait in a rainbow).

So finding transitional forms confirms a prediction of the theory, and establishes the continuum.

I’m not fussing about the theory of evolution but rather the fallacy of quantizing the continuum – pitch the fallacy and we don’t have a problem. But back to your point at hand, those fossils which were found were (and are today) quantized by consensus of scientists and inserted in a particular presumptive order as you say, to establish the continuum. That doesn’t make them any less a quantization or the continuum any more “real” than the quantization itself.

Whereas insisting that each "kind" is and always was unique is an example of the fallacy.

Again, if we apply your statement to the rainbow – there is no distinction between red and blue. When applied to abiogenesis, there is no distinction between life and non-life.

That is patently absurd and why I reject the appeal to the fallacy of quantizing the continuum to argue against abiogenesis.

The blending of colors in the rainbows does not prevent us from knowing red from blue in the rainbow much less in everyday life. The blending of fossils in the geologic record does not prevent us from recognizing the difference between a horse and a man. And none of the proposed theories of abiogenesis would keep us from knowing the difference between a rock and rabbit or a live cat and a dead cat.

Ichneumon: I agree with the first half (that it would be a fallacy to define a *particular* point in the continuum at which "life" suddenly exists where it had not at all existed a moment before), but I disagree with the second half, concerning whether this would mean that "abiogenesis is idle speculation". I don't believe that was tortoise's point at all. In fact, I think it might be the exact opposite: By trying to "see" a sharp dividing line between "life" and "nonlife", one would have trouble understanding abiogenesis, because one would be looking for a "poof" moment when life "suddenly" arose from "nonlife". But this expectation would be mistaken, since abiogenesis would be the *gradual* emergence of life-as-we-know it by the slow one-at-a-time accumulation of the *many* processes which, all together, make up the complex system that we are familiar with under the label of "life". Between a chemical "soup" and even the simplest modern single-celled organism would be many stages in the "gray area" between "nonlife" and today's "life" as we are used to seeing it. Only by understanding that there *is* (or if you prefer, "would be") a continuum of nonlife/life is one able to begin to grasp the concepts of abiogenesis in a meaningful way.

You should have kept reading the Plato thread. The geologic continuum was only one of the continuums being asserted!

There were layers of continuums of what lies underneath. We were splitting rocks and rabbits until there was no distinguishable difference – i.e. matter, subatomic particles, fields, geometry.

Frankly, it was absurd - the notion that life cannot be distinguished from non-life or death because all are made up of the same “stuff”. betty boop used the example of going to the top of the Leaning Tower of Pisa and throwing off a live albatross, a dead albatross and a 12 lb cannonball.

You also should have kept reading the Plato thread because, at that time, noone was trying to define the difference between life and non-life or death from the biochemical characterizations. That is, as you probably know, a creationist argument – and we were trying to investigate abiogenesis scientifically and objectively. The model we chose was mathematical, Shannon’s mathematical theory of communications.

Later, when we gave up on trying to discuss abiogenesis, we began looking at life v non-life or death in the here-and-now. At that time another mathematical model with biological characterizations was asserted by betty boop, the Irvin Bauer model.

But the arguments against being able to define life v. non-life or death became even more absurd. Namely, since we can envision artificial intelligence such as von Neumann’s probe therefore there is no difference between life and death/non-life. So we clarified that we were speaking to life which occurs in nature.

The assertion then was that life in nature is indistinguishable in terms of “higher” or “lower” lifeforms - amoeba is equal to man. Naturally, we found that absurd as well and pointed to a host of alternative theories for the rise of complexity in biological life – Kolmogorov, functional, self-organizing, physical, etc.

There were quite a few sidebars along the way but that is the gist of it.

The geologic continuum is the continuum of focus to Darwin. From it, he asserted a continuum of biological life, common descent. But that is only one of the continuums involved here. And the conclusions being drawn right and left by asserting continuums and decrying quantizations are patently mindless.

Everyone knows there is a difference between life and death and between life and non-life. Everyone knows there is a difference between lifeforms. If they didn’t, they’d be moving to ban antibiotics and grant equal rights to bacteria.

It is the argument itself – the fallacy of quantizing the continuum - which is absurd, a smokescreen which prevents serious investigation of important issues here on the forum.

Physicist: Sophistry. Evolution is of course quantized at the level of the individual. The fossil record is of course tied to that quantization, because fossils are necessarily the remains of individuals. To claim that that disproves evolution is a farce, because it could not have been otherwise.

Indeed. It was sophistry – an attempt to make a point, hopefully with a little humor attached.

The fallacy of quantizing the continuum – this continuum, that continuum, all the continuums – was being thrown around like smoke bombs and obfuscated the issues we were trying to discuss.

But two can play that game – so I volleyed it right back to y’all by applying the fallacy of quantizing the continuum to the theory of evolution.

In sum, it is not possible for us to describe a rose and not be able to use the names of colors because their boundaries are obscured in a rainbow. If we say that green is made up of yellow and blue – the fact that green, yellow and blue all occur in a rainbow somewhere sometime – does not make it any less clear that green is made up of yellow and blue.

[discostu]

The hardware folks and OS folks have done wonders for the rest of the industry. Back in the day all programmers had to know all this stuff, if you wanted your program to print a document you better know how each individual printer you wanted to support worked, saving data meant going through what you went through, graphics were a stone bitch. It's a much nicer industry to work in now when you can handle most of this stuff (except for high end graphics) by simply telling the operating system to do it. Looking back on the industry it's amazing what we've done, one of my instructors in school had been around so long she actually worked on a computer that was programmed with wires, making the physical connections, the pre-cursor to programming in machine language, it's amazing that at that point in time people actually tolerated working in the industry long enough to move it forward.

And while we're at it thank God ISA is dead, what a PITA.

[js1138]

You seem really upset that the definition of life is not settled. Please calm down and try to understand why this is so.

It is not difficult to determine that an entity is the offspring of a living thing. DNA and RNA are giveaways. It is also not difficult to determine that an individual that used to metabolize has ceased to metabolize. (Except for viruses, which never did, and spores, which have suspended metabolism.) So except for the trillions of bacteria that are able to to suspend animation and reanimate under more favorable conditions, it is fairly easy to distinguish living from dead.

But if there is a chain of chemical evolution leading to life, and if we can reconstruct it (or one of the possible chains), it will be difficult to determine which step is uniquely the first living entity.

Without that history, or a plausibly reconstructed history, we don't really know how easy or difficult it is to define life.