Still More Evidence for Evolution 1482
Uche writes: "Biologists at the University of California, San Diego have uncovered the first genetic evidence that explains how large-scale alterations to body plans were accomplished during the early evolution of animals."
Re:Evolution WILL happen (Score:1, Informative)
Explain a lot but... (Score:4, Informative)
Re:Not "more evidence for evolution" (Score:2, Informative)
Not quite. Fact: Charles Darwin was born in 1809. The Origin of Species was first published in 1859. People started believing it right away. By 1925 the matter was already in U.S. Courts (the Scopes "Monkey Trial").
It's also not true that scientific method only allows for disproving a theory. Duplicating an experiment or obtaining corroborating evidence bolsters a theory.
Re:Not "more evidence for evolution" (Score:2, Informative)
Stipulative Definitions (or) formerly: jargon.
Scientist: Law == invariant relationship between cause and effect. (final version)
Layman: Law == another $100 on taxes
Scientist: Theory == proven, widely accepted principle or explaination (release 1.0)
Layman: Theory == weak explanation
Scientist: Hypothesis == working theory, subject to revision (beta version of a theory)
Layman: Hypothesis == Theory
Scientest: Conjecture == guess (alpha version of theory)
Layman: Conjecture == ??
In science, everything must be questioned.
"Marge, I agree with you -- in theory. In theory, communism works. In theory." -Homer Simpson
Re:Explain a lot but...- Origin of wings (Score:2, Informative)
It has been suggested that wings were solar panels, turned into gliders and later, wings.
A theory that i find more plausible is that wings developed from gills in aquatic insects, and the transitional stages were used for skimming the water surface. Such gills are found on living insects like mayfly larvae, and they already have all the musculation and control nerves in place.
Re:Irreducible Complexity (Score:2, Informative)
Unfortunately, this article and its examples are inadequate. Just because you cannot imagine how something could have evolved, doesn't mean that it couldn't have done so.
The author of the referred article insists that we understand each part of the structures which he describes as irreducibly complex, but he also implicitly presumes that he completely understands their history, and that it's completely linear. In fact, his whole argument hinges on his understanding the entire history of these "irreducibly complex" structures. That actually begs the question. You can't presume history to prove that same history.
I'd like to use his own mousetrap example (of something that couldn't have evolved) to counter his point.
Imagine a springlike structure with a completely different function, perhaps a stiff spine for protection. Imagine then that there are circumstances where that structure catches slightly while under tension, but can be released with some force. Ever had a sticky accelerator pedal?
Once that catching proves evolutionarily useful, then it might eventually develops into a relatively sophisticated release mechanism.
The mousetrap would not have been only a mousetrap through all of its evolutionary history.
In fact, I suspect that there are multiple mousetrap like structures out there in the biological world.
In the game of Life, there are what is known as Garden of Eden patterns, because there is provably no way that these things could have developed from any predecesor structure based on the rules of the game. In real life, we don't know all the rules.
Oh, and: Fundmentalist materialist? Are you trying to be insulting by calling me a fundamentalist? I'm certainly foolish for indulging in a scientific argument with someone for whom religious tenets are postulated as facts.
Re:OK then, Intelligent Design (Score:2, Informative)
I think he's a little too eager to declare the issue resolved in favor of molecular design, though. I can't argue that evolution presents a well-formulated answer to these problems, but I don't see any reason why it can't or won't, eventually.
That's pretty much the science version of "the check's in the mail", isn't it?
Behe answers your point thusly:
"I agree with the commonsense point that no one can predict the future of science. I strongly disagree with the contention that, because we can?t guarantee the success of intelligent design theory, it can be dismissed, or should not be pursued. If science operated in such a manner, no theory would ever be investigated, because no theory is guaranteed success forever. Indeed, if one ignores a hypothesis because it may one day be demonstrated to be incorrect, then one paradoxically takes unfalsifiability to be a necessary trait of a scientific theory. Although philosophers of science have debated whether falsifiability is a requirement of a scientific theory, no one to my knowledge has argued that unfalsifiability is a necessary mark."
(http://www.arn.org/docs/behe/mb_philosophicalob je ctionsresponse.htm):
Best,
-jimbo
"Positive" Mutations (Score:3, Informative)
This isn't true at all really. Granted, we might never have zapped an E.coli with enough UV light to make it grow arms, but we've certaintly gotten plenty of positive function out of mutations in labs.
For instance, there is a well known tool in microbiology known as the "Temperature-Sensitive Mutant". A good way to get one of these is to zap it with UV or some other mutagen to induce a random point mutation (change in one nucleotide). This could alter the gene product just enough to make it non-functional at high temperatures, making the organism more sensitive to the environment than it was in the wild type form. This new sensitivity is a gain in function for the organism. It might not be beneficial, but it is a demonstrable gain of ability for the organism.
Another example would be oncogenes, which aren't always active, but can be activated via mutations, causing cancer.
There's some foddder for your next debate. Remember, a positive gain in function may wind up killing the organism, which is one reason why evolution takes so long. But random mutations certaintly have been shown to have an affect beyond deletion of the gene.
Re:Well done lads, collective pat on the back (Score:5, Informative)
Regarding your First Amendment Arguement, you're totally wrong. You have the right to say you believe in Creationism and Evolution is rubbish. However, that right does not extend to forcing schools to teach your opinion. End of Story.
Finally, I would like to make it clear that I am a Christian and believe God is quite responsible for the creation of the Universe and mankind. However, I refuse to take 7 days literally and admire the fine tuning of a Universe which expands gracefully; a planet formed out of star bits to contain the ingredients for life; and the effectiveness of evolution. If you witnessed the Big Bang, what better description than "then there was light"? I digress. I would encourage you to accept scientists when they tell you their description of the world is kinda close to how it actually is. Then admire the brilliance of the universe that was Created. Huge, billions and billions of stars all created with an attention to detail that makes quantum phyisics a mess for us.
Enjoy the world and stop whining that science shows a description of creation targetted to a civilization 4000 years old as much as to modern man, might not be best taken literally.
Re:Honesty - not! (Score:3, Informative)
> This particular problem has frequently been pointed out by creationists, but evolutionists have dismissed it as a non-issue. Until now. Now when they have found an answer to the problem, it suddenly makes sense to address the issue.
You seem to be unaware that scientists have been growing insects with extra body segments, legs sprouting from their heads, etc., for decades now. All the quoted text means is that they have found the built-in mechanism for managing this, not that they have suddenly discovered that it is possible.
Thank you for showing the lurkers how bad creationists are about twisting everything around in hopes of discrediting science, and how pathetic that spin control is when you dissect it.
Positive Mutations & Antibiotic Resistance - c (Score:4, Informative)
From the FDA Web site The Rise of Antibiotic Resistant Infections [fda.gov]:
The increased prevalence of antibiotic resistance is an outcome of evolution. Any population of organisms, bacteria included, naturally includes variants with unusual traits--in this case, the ability to withstand an antibiotic's attack on a microbe. When a person takes an antibiotic, the drug kills the defenseless bacteria, leaving behind--or "selecting," in biological terms--those that can resist it. These renegade bacteria then multiply, increasing their numbers a millionfold in a day, becoming the predominant microorganism.
Re:Troubling (Score:5, Informative)
Belief? I don't believe in evolution -- I wouldn't know how to do such a thing. Belief never comes into it.
The preponderance of the evidence leads me to an obvious conclusion -- changes in individual living things occur from generation to generation. Enough time and changes occur, and you have this thing called evolution. In some ancient businesses, it's just called breeding.
If that evidence wasn't there, I'd conclude differently...but not necessarily that a spirit or deity was the necessary other choice.
Evolutionary Math(Dawkins is a Fraud) (Score:4, Informative)
Every environment can be thought of as presenting a utility function to the organisms that inhabit that environment. Dawkins gives an example of the following utility function:
Try to see if a population of organisms can "discover" the line of poetry "This is the way the world ends, not with a bang but a whimper." You'll note that there are 29 possible choices for each letter (26 letters + commas + periods + spaces). And in the above string, there are a total of 62 characters. So, to present the power of evolutionary theory, Dawkins imagines a population of agents randomly initialized to 62 characters. One of these might be:
"jkdzcn43asdf lkjasdfhaokjshfla ksdhfoiuykjahs, asdasd. sdfsdf."
you can imagine that each agent reproduces unequally based upon how well it does given the utility function -- in this case, the utility function returns an integer from 0 to 62, where 0 indicates no letters match and 62 represents a perfect match for the entire sentence. Each generation is exposed to mutation in the Dawkins example, though one could easily add crossover (which implies sexual reproduction) and inversion. The code is roughly:
1) initialize X agents in a population to random strings of length 62
2) write a function where each agent reproduces unequally based upon how well it optimizes the utility function given above. This choice matters, but not a lot. For our purposes, imagine that every organism below some threshold X has a 10% chance per time period of dying outright. And every organism above this threshold has a 10% chance of replicating.
3) After step 2 (which represents one tick on the clock), expose each organism to genetic operators. Mutation is simple: pick a % chance Y (where Y is small; if it is too large, you lose information too quickly) for each character in an agent (or gene if you prefer) to mutate to a random character. Thus, if Y is equal to
4) repeat steps 2 and 3 until you see equilibration of your population.
After a bit, it should be obvious to you that most of your agents will approach the correct sentence, whatever their starting values. Further, not all of the organisms in a population will ever be at the "right" outcome, given mutation in step 3.
So what does this tell us? Simple math helps out. To optimize the utility function above is simple, and we know this because we can compute the number of steps it would take to optimize it. Couple of points:
1) the function Dawkins uses (outlined above) is separable. No character / gene depends upon any other character / gene to determine the utility of its expression. This is huge. Think about it until you get a smile on your face. For real organisms, this is NOT the case (i.e., genes are non-separable). This is why evaluating the results of the genome project is ugly. If we had, for example, one gene acting alone to determine intelligence, it would be easy to detect / modify. Sadly, multiple genes acting in concert determine intelligence, and modifying one gene in the set changes the value for the entire set.
2) The number of steps needed to optimize the above function is 29 * 62 = 1798, which is an extraordinarily TINY search space.
3) If the characters / genes were non-separable, as they are in real organisms, things are quite different. Worst case is completely non-separable -- i.e., every character depends upon the value of every other character for evaluation under the utility function. In this case, you have 29^62 (where the '^' represents the exponent function). Obviously, this is a freaking HUGE number. Even low levels of non-separability (e.g., pairs of genes that depend upon each other to produce a trait) generate huge search spaces.
The fraud of Dawkins is thus simple. He proposes a set of operators that
define his theory of evolution -- unequal reproduction, crossover, mutation,
and inversion, and illustrates their efficacy (i.e., the "success" of the
theory) on a simple toy problem. The ugliness, however, is that solving
separable problems, which is the class of utility functions Dawkins uses
to "test" his theory, is trivial. Everything / anything works well on them,
and there is no real way for any given theory to fail on this class of
utility functions. The other, more interesting class, which has the
property of being an analog to REAL ORGANISMS WITH REAL GENES is when the
utility functions are non-separable, and the theory / set of operators
Dawkins proposes has NO success searching the spaces induced by this type of
utility function.
It is as if I set up a craps game, you come to play, and the rules are, I
win all double sixes and you win everything else. You commence to roll
double sixes until I have all the money in the world. I assert that the
dice are not loaded.
The dice for complex life are loaded somehow, or we don't understand the
mechanisms of genetics. The existence of these regulator genes simply begs
the question.
None of this, of course, displaces evolution as the best fit for the
available evidence.
Karl
Re:Evolution WILL happen (Score:2, Informative)
Not true. Take a set of photographs of people ranging from supermodels to severe facial deformities, and show them to people from around the world, regardless of culture, education, location, or the amount of isolation, and ask them to arrange the photgraphs in order from most to least beautiful.
It's the same order every time. Our sense of beauty is directly involved with our ability to measure symmetry. Symmetry implies health, which is attractive.
Re:Control genes (Score:2, Informative)
IANABC (I am not a bio-chemist.)
I have always wondered how breeders could come up with so many wildly different breeds of dogs. Then I saw a short interview on a science show that addressed this question. The guy said the reason dog breeders could breed more varieties of dogs than, let's say, cat breeders could breed varieties of cats, was that dogs already had a particularly rich genetic heritage to play with. The opposite of cheetahs, for instance,
whose genetic variance is so slight they could
all serve as organ donors for one another.
As for dogs being helpless in the wild, haven't you heard of feral dogs? I understand they are a big problem in some parts of the world.
Look like dogs, act like coyotes.
Re:Evolution WILL happen (Score:2, Informative)
It's the same order every time. Our sense of beauty is directly involved with our ability to measure symmetry. Symmetry implies health, which is attractive."
Symmetry is a factor, but it's not the only one. There are huge cultural differences in how we perceive beauty. One of the most obvious is the question of weight. In America and other Western nations, there is a major emphasis on thinness as a factor in feminine beauty, and a somewhat lighter emphasis for men. But in many other cultures, fat men and women are considered attractive.
This changes quite a bit over time, as well. In the first half of this century, and in many eras before, heavy women were considered highly attractive. If you don't believe me, watch a movie with Mae West, or check out some of the paintings of Botticelli.
Evolution Must Be Banned! (Score:1, Informative)
You can send an E-mail to Senator Hochstatter from a form at: Senator Hochstatter [wa.gov]
Re:Explain a lot but... (Score:2, Informative)
This [ncsu.edu] gives some related information on evolution of insect wings.
This [nurseminerva.co.uk] talks about it some too.
This [google.com] is where I left off looking.
Re:Positive Mutations & Antibiotics (Score:2, Informative)
Re:Evolutionary Math(Dawkins is a Fraud) (Score:2, Informative)
2) Dawkins was merely using a simplistic example to demonstrate the idea of cumulative evolution that builds on itself vs. instant evolution from the original to the final result. He was pointing out the fallacy of those who mistakenly believe that the theory of evolution implies single-step mutations from one species to the next. He wasn't trying to show a realistic model of evolution.
3) In that book, (I think) he also describes how some genes are turned on or off by the environment they're in. E.g. in a skin cell, the local environment is much different than in a neuron, so even though both cells have the same genes, they are very very different. Different genes are expressed in different orders with different results. A group of genes doesn't code for say, green eyes, it makes a certain protein in a certain circumstance, perhaps a different protein in a different circumstance. In one cell the protein might cause one action, in another cell, in the presence of some enzyme or what have you, it might cause a totally different one. So in the embryo, a gene in one place can easily hugely affect the outcome of the organism, since each subsequent descendant of that cell would be in a slightly different environment than it otherwise would have been in.
There is unbelievable complexity in all this. Tiny changes here and there have the potential to make big differences.
Re:You do live a sheltered life, don't you? (Score:2, Informative)
Basically, most of the lines of thinking come down to this precept: God created Humanity with Free Will. We are able to do as we choose, for good or bad, right or wrong. God didn't create us to be automatons, He created us in His image (and, seriously, God can do whatever the heck He wants) and thus we were given the critical choice of "follow God or follow self". Adam & Eve chose Self and thus, the mess we're in.
It's a bit of a "you made your bed, now you've got to lie in it" sort of thing. It's not that God doesn't care, it's that we must reap what we (collectively) have sown. His solution to this was sending His Son to die as a "sin proxy/firewall" for us; that is, Jesus took care of the everlasting punishment for us. But we still live in a broken world and so must live with the impacts of humanity's brokenness until we shuffle loose this mortal coil.
Re:evolution of the eye (Score:1, Informative)
> macro-evolution is pretty questionable at best.
Methinks that your problem is that you, like so many people out there, know nothing about evolution by natural selection but somehow reckon that can issue authoritative statements on what is, or is not, evidence.
> Someone explain to me, for instance, how such
> an intricate device such as the eye evolved
> randomly.
This pet objection from creationists has been so thoroughly debunked so many times in so many books that I find it surprising that anybody still is coming up with it. Have you tried to read any of the standard textbooks on the subject?
> It couldn't have come together piece by piece, > since anything less than a full eye would be
> useless and "selected" against
Wrong! Partial sensitivity to light, as compared to no sensitivity at all, is an obvious source of adaptive advantage, in the right environment, and will be naturally selected.
You realize that you know nothing about the subject?
> So a mutation, somewhere along the way,
> produced a full-fledged functioning eye?!
Strike three! Such macromutations are not possible.
You are out! Do you still think that you don't need to to read something about the subject?
> Color me skeptical.
No, color you ignorant - an altogether different state of affairs. Skepticism involves a certain degree of savvy whic is not present here.
I would like to contribute to your learning process, letting you know that, not only has the eye been evolved by natural selection, but it has been evolved several times, independently: you might enjoy learning that invertebrate eyes (like those of squids) are totally different from vertebrate, or insect eyes.
Just One Major Bone to Pick (Score:3, Informative)
I normally like to argue points on direct (as opposed to indirect) merit and avoid foul language and name-calling since it thins the argument, sometimes unacceptably.
That said, go out and read a fucking book on physics, you moron. I get so so SO tired of this stupidity that I have to lash out. Evolution does not contradict the second law of thermodynamics, in the same way that a refrigerator does not contradict the second law of thermodynamics. The Sun pours out an astonishing amount of energy, and what little of that energy falls on the Earth provides very nearly all of the energy to drive every living thing (and most non-living things) on the planet.
Now say it slowly, so you get it. Local reduction in entropy, coupled with larger general increase in entropy, is not inconsistent with the second law of thermodynamics.
Please repeat until you actually grasp it. Thank you.
Virg
Re:Can Side-show Shrimp Survive? (Score:2, Informative)
You'll notice of course that the 3 pair shrimp could be less well adapted to whatever the niche of the 20 leg pair shrimp was and still out-compete the 20 pair shrimp just so long as the advantage of needing less resources and reproduces faster outweighs whatever advantage the 20 pair shrimp has an an individual
Lots of variations you can play on this one - the above assumes that to 20 and 3 leg pair shrimp continue to live in exactly the same ecological niche - which ain't necessarily so
if you don't believe in evolution, explain this: (Score:2, Informative)
Anyway, In this article they do a rigorous analysis of the data on olfactory receptor (OR) genes from the recently acquired mouse genome compared to the data from the human genome project. I forget the exact numbers, but mice have about 1000 OR genes. Humans have about the same number, but something like 75% of ours are pseudogenized. Basically, this means they've been converted to pseudogenes, or sequences in the genome that obviously used to be functional genes but have mutated to a nonfunctional state. This much was known before. In this paper, however, they use techniques based on similarity of sequences to group the mouse OR genes into families and subfamilies. Then they group the human OR genes into the same families. To sum up what they found, if you were to take a random group of say six mouse OR genes, there will be five or six human genes that are the human counterparts of those mouse genes (over 90% of human OR genes have a mouse gene that's over 95% identical at the protein sequence level, and 77% have a mouse gene that's over 99% identical, so reliable identification is not a big issue). However, within that group of five or six human genes, all but one of them has been converted to a pseudogene. They find this over and over again. There's only one functional gene in each group. Each group, BTW, can be thought of as sensing when a certain class of feature is present on a molecule. In an analogy to vision, it would be like if mice could see different shades of six types of red, but we could see only shades of one.
Okay, here's an evolutionary explanation. A long time ago humans were monkey-like animals. Before that, dog-like animals, before that mouse-like animals, etc. Whatever animal we used to be, it was heavily dependent on a highly-developed sense of smell for survival (hence an entire 2% of our genome being dedicated to it--think about that). However, as we progressed evolutionarily, having an exquisitely sensitive and precise sense of smell became less and less important, but smelling things in general was still necessary. The genes mutated and mutated, but if the last member of a family became pseudogenized, that would compromise our ability to smell molecules with a certain class of molecular features (by analogy, if we couldn't see red at all), and those pre-humans would die. As a result, we're left with the HIGHLY nonrandom distribution of working genes. I want to point out that while this could be written off as "microevolution," consider two things: #1- all humans on earth will turn out to have >98% identical OR genes. #2- I say this because that nonrandom of a pattern with that many genes involved would take a LONG time to evolve, or at least a lot longer than humans have been on different continents. Almost certainly longer than we have been Homo sapiens.
Can anyone come up with a non-evolutionary explanation that explains 1) why so many of the genes are pseudogenized, 2) why the selection of which genes are pseudogenized is so highly nonrandom and optimized for the real world? I'm not asking for a critique of my evolutionary explanation, as the reasoning as I've presented it is not intended to be bulletproof. However, I do think that the underlying model is correct and I don't think there's any better explanation.