Microbiology, biochemistry, and Evolution

[OnlyAmbrose]

Sorry to start a new topic, but I wanted this one to be separate. I understand that the main evolution topic has quite a few philosophical dissertations and I want to be as specific as possible in this one. This may have actually been brought up once or twice in it, but I definitely don't feel like searching a hundred pages to find out.

Soooo... as prologue, a lot of you on both sides of the debate probably know that I've generally taken the stance that evolution is clearly a theory well supported by science, and therefore I, like many Catholics, accept it.

Well, a curious thought popped into my head a few weeks ago, and in the time between now and then I did some reading which has led me to question the concept of macroevolution being the cause of the complexity and diversity of life today.

In essence, I was by chance reading a wikipedia article about cell structures and bacteria, etc. I was fascinated by the biochemistry of it all. Processes in cells are much like processes in robotic factories. All a cell is is just proteins and molecules reacting in a certain way; there's no intelligent body directing it, and yet somehow it manages to work in an almost cosmopolitan or factory-like way.

In my mind it didn't seem to add up that 3.7 billion years worth of natural selection could ever add up to a structure as complex as even a bacteria, let alone ultimately create structures composed of many of these already complex little bodies into even more complicated systems. This was just a hunch, but I decided to follow it up with some reading.

So I did some basic research on biochemistry. By my basic understanding, molecules don't "think", they just react to each other in certain ways; they fit together due to shape, attract due to charge, etc. Cells are made up of these molecules, especially proteins. Proteins then combine to make insanely and irreductibly complex structures with moving parts. Factories, transportation systems, etc.

I don't think that natural selection can adequately explain the complexity of a cell. They're just composed of too many complex parts. Remember that natural selection only preserves traits that are beneficial to an organism, ie traits that give it an advantage. Each intricate part of a cell is composed of several different specifically arranged proteins; oftentimes a structure is composed of parts which are composed of even more parts which are composed of constituent protein.

But how could natural selection preserve these otherwise useless parts? Darwin was fairly specific in saying that natural selection is a slow process; organs and structures don't just pop up in one generation. It takes time for certain small mutations to occur. So in order for this to fit with natural selection, it would mean that each individual part must be present in the cell for some reason or another. But there would be no reason for that part to be present at all because alone each part is useless, so natural selection wouldn't preserve it.

These are just my thoughts so far, and in my reading I was surprised to see an oddly large amount of biochemists who used this data to become evolutionary skeptics. As a guy who's been an evolutionist for years, I'd like to know how Darwinists explain the evolution of these microorganisms. After all, the complexity of a cell is so immense that some mathematicians estimate that the chances of some of the structures occurring by chance in the amount of time life has existed is about nil. That said, there are many such structures in existence in the cell, not to mention many such structures within multi-celled organisms as well! The odds against evolution just seem staggering to me, the more I research biochem.

[MeDeFe]

There's just one thing I wish to note.

Natural selection does not, I repeat: NOT, only preserve traits that are beneficial to the organism and to the number of organisms it can spawn in order to pass on its genes. Beneficial traits are more likely to be passed on from one generation to the next because organisms possessing these traits will on average be more successful, detrimental traits are less likely to be passed on from one generation to the next for the inverse reason, and as for neutral traits, well, find a mathematician to help you with calculating the probabilities, I'm not sure I can do it adequately. It depends on how widespread they are among the given population, how "close" to a beneficial or detrimental trait they are and a lot of other factors as well.
Also, if a detrimental and a beneficial trait are more likely to be passed on together than not, the detrimental trait might persist more or less indefinitely within the population.

Notice the "from one generation to the next", that means generations of the whole population, it says nothing about what traits any given parent organisms will pass on to their offspring.

[Neoteny]

NO AMBROSE! NO! PUT DOWN THE BEHE AND SLOWLY WALK AWAY! Anyhow, I believe the term you were looking for was "irreducible complexity." That's the phrase that has been coined, anyhow.

In all seriousness, it really is mind boggling to think that natural selection produced the complexity we see today. Having studied the microbiology aspects first hand, I can definitely see where this can come in. But we can't let the timescales that we are used to cloud our judgment on this matter. Take what my clever friend above said, and apply if over billions of years, and you can get what we see today. Really think about how long 3.7 billion years is, before you toss it aside. Also, compare that amount of time to the reproductive speed of bacteria in particular.

I can't really say anymore without some kind of specifics, but I'd be happy to go back and forth with you, if you like.

[AlgyTaylor]

This book will go a long way to explaining the questions you're asking.

[tzor]

The evolution of microorganisms is an interesting subject. I admit that this is not my field of expertise (BS Physics, MA Comp Science) but my physics background does show me where poor assumptions can lead to resistance to certain ideas, specifically a broad misunderstanding of the laws of thermodynamics. In short it is possible for something to appear to become more complex over time because the structure itself is actually a higher form of entropy than the previously “chaotic” state prior to the process. The formation of crystals from cooling of molecules is one example of this apparent violation of entropy.

So systems form all the time. Some work, and some do not work. We never know about the ones that don’t work; only about the ones that work. Given time these systems can develop into self replicating structures and then KABOOM.

Well at least until the next best thing comes along, or when shit happens on a massive scale or when the environment mutates ever so slightly. The first major life forms (anaerobic) were almost completely exterminated by the second major life forms (aerobic) because the bi-product of aerobic life forms (O2 from plants) was poison to anaerobic microorganisms. Today they are found only at the extreme bottoms of the ocean.

The notion that given this complex biological super computer that complex structures develop is a perfectly reasonable assumption. One only has to look at modern evolution of bacteria and viruses to see how even a small population of survivors can easily replicate the population again especially when competition has been eliminated.

When we scale up to larger organisms we find a “complexity” of systems but they are all derived from a basic cell system. Each organ is developed from two factors. The DNA does play a part but development is strongly influenced by chemical and environmental factors. Not all the organs in the body are strictly necessary. Dinosaurs ruled the earth without a single diaphragm in part because the O2 content of the atmosphere was higher. Sharks still swim the oceans without the need for kidneys.

Understanding that organ development is not just a complex collection of structures determined solely by DNA but a series of associations that are directed by DNA and by both hormonal and environmental conditions takes a little getting used to. Consider the differences between male and female which seems like it requires a lot of genetic engineering (although the difference between X and Y is like half a chromosome). Guys have a prostrate right but what do the gals have? (Answer: Although not realized until recently due to a lack of significant study on odd areas of the female anatomy the equivalent organ is called the urethral sponge.) Even things that seem vastly different (like hair on mammals and feathers on birds) are actually minor changes in the ways the structures develop.

A few centuries ago a man stared into the sky and saw lines on Mars. He called them rivers which got badly translated as canals. This implied that there was intelligent life at work and by extension intelligent life on Mars. There was intelligent life alright, but not on Mars. It was on Earth where human minds had evolved the process of recognizing patterns even when the image was actually random. And that’s the problem with looking for intelligence … one only need a mirror to find it.

As some alien on Star Trek once put it, we are “bags of mostly water.”

[Snorri1234]

In my mind it didn't seem to add up that 3.7 billion years worth of natural selection could ever add up to a structure as complex as even a bacteria, let alone ultimately create structures composed of many of these already complex little bodies into even more complicated systems

I can spot the problem now already.

[suggs]

Ambrose, your lenghty post can be summed up as "Whoah, it all looks too complex to be explained by evolution!"
Fraid not - it just means you (and I) dont understand it.
In fact, you are (unknowingly or not, I cant say) sneaking in the Teleological argument.
To sum up -the world is so beautiful, and so complex, SOMEONE must have designed it (hence its also called the argument from design).

But Hume demolished this argument some time ago, and its been demolished in other threads, so I wont digress too much here.
Suffice to say, amongst MANY other crticisms, your point can be answered thus:

"NAH, IT COULD JUST BE RANDOM, MATE".
Sorry to burst your bubble.

[PLAYER57832]

No one currently suggests that natural selection alone accounted for the diversity.

First, mutations and such are not fully random. Nor is natural selection precise. Sometimes it isn't the "fittest" that survives. Sometimes the fittest buck gets hit by a landslide ... or some such.

Also, you had a whole series of catostrophic events causing die-offs. Debate rages over why (as in cause, not moral "why") and how they happened, but not that they happened.

After the events, there was, essentially a lot of change and a lot of "free space" available. So, things spread out and diversified "relatively" quickly.

In fact, many suggest we are in such an upheaval right now. Witness the change in various livestock and plant crops... not just now with actual genetic manipulation, but in years past where plain old breeding was the tool. You can absolutely argue that these were human manipulations. But, those changes occured in a mere hundreds of years. Evolution took tens of thousands even at its most rapid.

[tzor]

"NAH, IT COULD JUST BE RANDOM, MATE".
Sorry to burst your bubble.

I have a hard time believing that this is all truely random. After all, people have been complaining about how CC dice is far from random so I tend to suspect that everyone including the universe uses unrandom dice.

[MeDeFe]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

[Neoteny]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

Can you imagine how quickly GD would degenerate into frothy-mouthed convulsions? It would almost be like here.

[MeDeFe]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

Can you imagine how quickly GD would degenerate into frothy-mouthed convulsions? It would almost be like here.

Yeah, there are drawbacks as well, 6s are obviously fitter and at some point all the rolls will be 666 vs 66.

[Neoteny]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

Can you imagine how quickly GD would degenerate into frothy-mouthed convulsions? It would almost be like here.

Yeah, there are drawbacks as well, 6s are obviously fitter and at some point all the rolls will be 666 vs 66.

Eventually, the red dice would turn into white dice, and almost everyone would starve to death as genetic drift mixed things up a bit until a small population would survive long enough to bottleneck itself out of existence. Wait, is that right?

[MeDeFe]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

Can you imagine how quickly GD would degenerate into frothy-mouthed convulsions? It would almost be like here.

Yeah, there are drawbacks as well, 6s are obviously fitter and at some point all the rolls will be 666 vs 66.

Eventually, the red dice would turn into white dice, and almost everyone would starve to death as genetic drift mixed things up a bit until a small population would survive long enough to bottleneck itself out of existence. Wait, is that right?

I'm not sure whether white and red dice can interbreed or whether they are to be considered completely separate species, and if the trait for red is dominant which is implied by the fact that defending dice win on a tie I feel that an equilibrium might emerge.

[Neoteny]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

Can you imagine how quickly GD would degenerate into frothy-mouthed convulsions? It would almost be like here.

Yeah, there are drawbacks as well, 6s are obviously fitter and at some point all the rolls will be 666 vs 66.

Eventually, the red dice would turn into white dice, and almost everyone would starve to death as genetic drift mixed things up a bit until a small population would survive long enough to bottleneck itself out of existence. Wait, is that right?

I'm not sure whether white and red dice can interbreed or whether they are to be considered completely separate species, and if the trait for red is dominant which is implied by the fact that defending dice win on a tie I feel that an equilibrium might emerge.

This sounds like a job for one of those population modeling programs...

[jonesthecurl]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

Can you imagine how quickly GD would degenerate into frothy-mouthed convulsions? It would almost be like here.

Yeah, there are drawbacks as well, 6s are obviously fitter and at some point all the rolls will be 666 vs 66.

What, the Devil vs Rock 'n' Roll??

Surely they're on the same side...

[tzor]

An idea begins to emerge: The CC dice should be based on natural selection in order to achieve randomness.

If CC dice used evolution and natural selection soon the 8 sided dice would exterminate all the 6 sided dice. In turn they would be defeated by the 12 sided dice and finally every game would use 20 sided dice.

If we used un-natural selection then non polyhedral solids could be conisdered including the d100.

("THE OPPONENT ROLLED TWO '00' IN A ROW ... THE DICE ARE NOT FAIR!")

[OnlyAmbrose]

NO AMBROSE! NO! PUT DOWN THE BEHE AND SLOWLY WALK AWAY! Anyhow, I believe the term you were looking for was "irreducible complexity." That's the phrase that has been coined, anyhow.

It showed up in an article I was reading on criticisms of Darwinism. This Behe guy seems highly contravercial.

I'm doing more research before I comment on the matter again. I'm more or less undecided at this point.

tbh I've never really researched evolution before this point. Y'all may have noticed that I've mostly steered clear from evolution threads, mostly because I don't really care one way or the other. And I still don't. As Kenneth Miller said of evolution: "to a person of faith it should enhance their sense of the Creator's majesty and wisdom." And I've always held to that point. But this whole issue of natural selection acting over a long period of time intrigued me, so I'm looking into it out of interest.

You can trust that my arguments for/against theism will remain largely cosmological and metaphysical, this is just a side-interest

[Jenos Ridan]

And that’s the problem with looking for intelligence … one only need a mirror to find it.

As some alien on Star Trek once put it, we are “bags of mostly water.”

At the risk of reveiling my utter geekness, I know the episode you are referencing. I gave up on The Next Generation for two reasons: truely bad science and blatant pseudo-utopian communist propaganda (eg: flawless society, no crime or poverty, etc.).

So, SETI has it all wrong?

[tzor]

At the risk of reveiling my utter geekness, I know the episode you are referencing. I gave up on The Next Generation for two reasons: truely bad science and blatant pseudo-utopian communist propaganda (eg: flawless society, no crime or poverty, etc.).

The initial setting of TNG turned me off because when they started pushing "kiddies in space." (They even had a kids contest where the lucky child would be in an episode.) Actually the "pseudo-utopian communist propaganda" was always in Star Trek, they just had better writers in the original series.

Consier this. What would you say was the purpose of Star Trek, or more precisely what would you write as the one line summary for the series. Here's my one liner. "Star Trek was the television series that made 'All in the Family' possible." By setting the scene in space the writers were able to bring up a number of hot button social issues of the day which could not be covered in any other manner due to the nature of censorship and regulation in the industry at that time.

The original series includes such topics as:

Racism - The half black / half white person chasing the other half black / half white person because they were the same color on the same side of their faces.

Overpopulation - The insanely pro-life planet where everyone was packed like sardines but they didn't want to practie birth control or kill anyone so they wanted to solve the problem by getting a major disease to diminish their population.

USSR - Yes that's what Klingons are for. Otherwise for comic relief you use Checkov. (He was always citing Russian historical revisionism.)

I retuned to TNG shortly after they killed off one of their characters (death by vile sentient oil sludge) because the actress dared to appear partly out of uniform in Playboy. The old series never bothered with continunity, (and most of the real utopian stuff came after the series had ended) and TNG was horrid at it. They ruined a number of polt points because of the inability to extend them across the seasons. The Q, the original Borg, are two examples of where in the old series you would use them and then promptly forget them. (Consider the race that literally ended the Federation / Klingon war by making all weapons too hot to handle. Once the epiode was over you never saw them again ... NEVER.)

[PLAYER57832]

NO AMBROSE! NO! PUT DOWN THE BEHE AND SLOWLY WALK AWAY! Anyhow, I believe the term you were looking for was "irreducible complexity." That's the phrase that has been coined, anyhow.

tbh I've never really researched evolution before this point. Y'all may have noticed that I've mostly steered clear from evolution threads, mostly because I don't really care one way or the other. And I still don't. As Kenneth Miller said of evolution: "to a person of faith it should enhance their sense of the Creator's majesty and wisdom." And I've always held to that point.

To person of faith, what is/should be critical is simply that God created all. I have long since come to the conclusion that the REAL "movers and shakers" behind the creationist movement have a completely non-religious agenda. Think about the consequences, the arguments put forth by strident creationists and follow that to "who will benefit". (follow the money...)

The truth is this is about discrediting science. Now, there are many, many, questions about the theory of Evolution (that all things evolved from simpler things which evolved from ... dust). But, evolution (that things change over time by various means, including natural selection) is fact. Though how much natural selection impacted Evolution can be partly debated (versus straight random events, intelligent design, etc.), that natural selection does occur is not debateable.

The sad truth is that this "debate" is allowed to take hold, not because Creation "science" truly presents a legitimate argument, but because folks don't know enough of science to see that they are NOT legitimate arguments. I mean, read through Widowmaker's thread ... and smatterings of those in support. Her primary argument is "Christians are not Evolutionists" ... when I pointed out that was completely false, she initially shut me down, saying that thread was "not about theological evolution". Well, gee, Athiests are still very much a minority in the US and most of the world, so that idea is just plain silly. BUT, it is what Widowmaker has been taught ... and believes.


Anyway, the microbiological examples are wonderful places to explore this because microbes have pretty short life spans. We can investigate the impacts of changes over multiple generations ... something much more difficult in mammals, reptiles, etc.

[tzor]

The truth is this is about discrediting science. Now, there are many, many, questions about the theory of Evolution (that all things evolved from simpler things which evolved from ... dust). But, evolution (that things change over time by various means, including natural selection) is fact. Though how much natural selection impacted Evolution can be partly debated (versus straight random events, intelligent design, etc.), that natural selection does occur is not debateable.

Evolution is not "Fact" but one can argue using Occam's razor, "entia non sunt multiplicanda praeter necessitatem", that it is the most simplist explanation out there and is the most correct explaination that we currently are aware of.

[Neoteny]

The truth is this is about discrediting science. Now, there are many, many, questions about the theory of Evolution (that all things evolved from simpler things which evolved from ... dust). But, evolution (that things change over time by various means, including natural selection) is fact. Though how much natural selection impacted Evolution can be partly debated (versus straight random events, intelligent design, etc.), that natural selection does occur is not debateable.

Evolution is not "Fact" but one can argue using Occam's razor, "entia non sunt multiplicanda praeter necessitatem", that it is the most simplist explanation out there and is the most correct explaination that we currently are aware of.

Really, nothing is fact. So what's your point?

[tzor]

Really, nothing is fact. So what's your point?

I won't go so far as to wander down the highway to nhilism, but my point is that to one extent evolution is a theory to explain a historical fact. History is an odd duck, science wise, as you can't go back in time to do experments. We often confuse solid theories with facts in the realm of history. It's like the question "what killed the dinosaurs?" We may come up with a number of explanations but none of them are facts. Aliens with laser rifles are probably going to be rejected offhand because there is nothing to suggest that might even have been possible.

This is why Occam's razor is most important. As Leonard Nemoy once said again and again in his famous series, "This series presents information based in part on theory and conjecture. The producer's purpose is to suggest some possible explanations, but not necessarily the only ones, to the mysteries we will examine." (On second thought I think that was a voice over, but I request permission to use artistic license.)

The question is not whether A is fact and B is not fact. The question is whether A is the most likely answer based on theory and those facts that are known and whether B hasn't got a leg to stand on. Because when we use the former, we risk the slippery slope of arguing for things that are weaker and weaker as equal absolute facts.

[PLAYER57832]

The truth is this is about discrediting science. Now, there are many, many, questions about the theory of Evolution (that all things evolved from simpler things which evolved from ... dust). But, evolution (that things change over time by various means, including natural selection) is fact. Though how much natural selection impacted Evolution can be partly debated (versus straight random events, intelligent design, etc.), that natural selection does occur is not debateable.

Evolution is not "Fact" but one can argue using Occam's razor, "entia non sunt multiplicanda praeter necessitatem", that it is the most simplist explanation out there and is the most correct explaination that we currently are aware of.

No, Evolution (big E) is not. However, evolution (small e) is ... things DO change over time. Also, as I said, there are a lot of facts to back it up. Where the "Creation Science" movement errs is in failing to distinguish between things that are proven and things that are up for question. I know you read at least some of Widowmaker's thread. If you didn't read the first few pages, do.

Are there possible challenges to Evolution? Abosolutely. In fact, I would argue that Darwin woudl barely recognize the theory in its current form. No Paleontologist talks about natural selection as a smooth progression anymore. And "survival of the fittest" has been modified to be more like "survival of the reasonably fit and very lucky". Etc.

If you want to bring in purpose/why, absolutely there is room for debate. Most Christians seem to be comfortable with something close to the Intelligent design, if it is meant to broadly be the idea that God designed the universe or set in motion the various factors, knowing the outcome. However most Christians also fully accept evolution. The group that is currently promoting Intelligent Design insist it has to be taught in opposition to/as an alternative to Evolution. Not as the "why" behind evolution, but they insist that evolution is strictly an athiestic theory and that this other theory is to be taught so Christian kids won't be taught the Bible is wrong. In reality, it is not about education, it is just one more attempt to bring their very narrow religious view of creation into science, to label it as somehow "equal" to the process of proof and validation that makes true science. It is not education, it is limitation. AND, the scary part is they are gaining serious ground.

From what you have said, you don't have kids, probably won't have any. So, this won't necessarily seem to impact you. However, the Bush administration is currently filled with large numbers of younger adults who were raised on these theories and these theories alone. Wonder how Bush could so readily dismiss Global Warming ... and various other environmental issues. Look at who is advising him.

At first, I did not worried much about Creationism. After all, freedom of thought and discussion is one of our fundamental values as a society. However, this movement is not about freedom of thought. It is not about truth or investigation of truth. It is about making sure that everybody thinks as they do. That alone is bad enough, but human nature. What makes this scary is that they try to pass off this as REAL SCIENCE ... and between the very ppor state of science education in our schools and the gigantic home schooling, they are quite succeeding.