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Quantum Evolution Poses Challenge to Darwinism
spaceorb writes "In his book, "Quantum Evolution", UK biologist Dr. Johnjoe McFadden asserts that life did not originate from the random movement of particles, simply because it is far too complex. Instead, he argues that evolution is a quantum system - genetic code exists in a quantum multiverse and cells are able to choose advantageous mutations. Click the above link for the story on UniSci; it's worth a read. "
Hard SF writer Greg Egan recently wrote a story about a similar idea in his book Teranesia. Check Greg Egan's Home Page for more informatino about the story and this fascinating geek/programmer/author.
God does play dice, and life was a lucky roll.
Some scientists seem desperate to find some theory - any theory will do - that might possibly explain the existence of life without the need to postulate a God. For a while, it was macro evolution - an extension of the micro evolution we all know, love and observe. That theory having been found wanting, they switch to a quantum sleight of hand - all mutations happen and, in some hand-wavy multi-dimensional way, the most beneficial (by whose judgement?) are chosen and the rest are discarded.
In this way, you can try and get around the mind-bogglingly massive unlikelihood of life ever coming into existence by chance (as the article recognises).
Forgive me if I don't jump in the air and scream "At last! Non-belief in God is intellectually credible! I can stop this Christianity lark and go out into the evil, bad world as an atheist with my intellectual pride intact..."
Gerv
Because we don't sense the passage of time while we didn't exist. For all we know, it took the creation and destruction of 1e512 universes of time before intelligent life happened to arise and we were able to think about the fact.
Now, if we happen to discover life on other planets someway, then we would be able to say how statistically probable life is. Until then, "probablistic" arguments are complete nonsense.
Not to mention that it doesn't argue against Darwin anyway. Darwin only poses Natural Selection (I believe) which is an observed, provable fact of biology.
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C'mon, this is something from a late-night, low-budget sci-fi show, not real science. This is mumbo-jumbo metaphysics -- there's absolutely zero science behind it. The "life is too complicated" argument seems to be the only one he's really got, and that one's pretty easily refuted by "well, here we are".
Physicists don't understand quantum mechanics.
Sure, it's complicated stuff. But people understand it a lot better than this guy does. We've got lasers that work, for example.
Today, one of the most popular interpretations, and one that has the backing of Nobel prize-winning physicists, is that there exists a multiverse in which everything that can happen really does happen -- but in parallel universes.
A fun explanation, and good for sci-fi, but I believe the "Copenhagen Interpretation" is more widely accepted -- essentially, particles not being observed exist in a state of probability waves. But anyway, if one is to accept this, this completely destroys the "life is too complicated" argument. Sure, it's complicated -- but even very small probablities have to happen somewhere in the "multiverse". And the only universes within which we'd be able to ask questions would be ones where that small chance happened.
Cells may enter quantum states when they are unable to divide and replicate and become isolated....
Um, no, that's when they d-i-e.
I haven't read the book, just the web article linked to above. But it sounds ridiculous to me. And the author is no expert in quantum mechanics -- he specializes in infectious diseases. Sounds like he read something about quantum mechanics in a pop science mag, and went from there.
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The article you have cited looks familiar to me: remember the guy who made fun of post-modernistic brabble writing an article heavily loaded with serious physic terms taken out of the context? This sounds similar to me: "quantum" is a nice, popular word, and using it out of the context and not in its proper meaning is nothing more then retorics.
As for a biologist, this whole article sounds like cheap boulevard sh*t to me. J. McFadden, OTOH, is a serious evolutionary biologist, publishing in good journals. He works as a theoretical biologist - as far I understand - with transposone mutagenesis. So maybe he did something interesting, and tried to make "a big thing" out of it - and notified some journalists, who got it wrong. There was a similar thing with the "theory of punctuated equilibria", which finally fitted nicely in the "synthetic theory of evolution" or "neodarwinism" (which is to darwinism in as much as quantum physics is to Newton's laws).
I am an evolutionist - and I certainly see possibilities for bacteria to judge which mutation could be better. There are some reasonable hypothetical mechanisms, which have nothing to do with quantum mechanics. Unfortunately, in spite of various tries and much research there are no convincing experiments. In most of the cases either noone could repeat the experiments, or better, easier explanations could have been found. Nevertheless, I do not see anything controversial about directed mutations: after all, the driving force of evolution will still be the natural selection coupled to other evolutionary mechanisms (like genetic drift). You have to have a broader view: most of the organisms try to influence the genes they passed to their offspring: for example, by coupling them to an other set of good genes - when choosing a good mating partner, who can demonstrate that he has good genes (for example, using the handicap strategy). You could say there already exists a kind of directional mutagenesis :-)
So much for the "controversy" of directed mutations. What I wanted to say is that there is no much incoherency with the current evolutionary paradigm (STE) per se. However, there is lot more on "sampling of the quantum space" and so on in the article you have posted here. Well, although I got some kind of introduction in quantum physics I cannot say I am fit in this field. However, I suspect strongly that people who are fit, are, on the other hand, not necessarily skilled in evolutionary sciences and molecular biology. I can't tell at this point: maybe this is something interesting, but to pose a challenge to the current model, a theory has to explain everything the former theory did plus a couple of other things plus do it more cleanly, more simply. I really don't know, but even if there is something in this quantum brabble I do not understand, it is only on the level of simple mutations and a very short time scale. OTOH, natural selection is known to work also on a larger time-scale.
One more thing left: the arousal of life itself. Well, one important point: the biologists have problems to tell how it happened not because they lack an explanation or a model, but because finding evidence for evolving molecules with a time scale of millions of years is unlikely to be found in sediments several billions years old, and unlikely to be demonstrated in an experiment, because such an experiment would take too long. However, it is not at all as unlikely as assembling a 747 by a tornado. Imagine a tornado that works for millions years on a planet covered with intact 747 parts; and if two parts get correctly assembled, they stay assembled and they propagate itself and produce they replica. Does it still sound improbable to you? What I really hate is biologists commenting on quantum physics like they were quantum physicists, physicists commenting on food science, and astronomers commenting on biology. Do I tell you how to program? ("Hey, you over there! C is obsolate! Use VB![*]). There are experiments with evolving and self-replicating RNA molecules; RNA is a nucleic acid which can both contain genetic information and act as an enzyme. Compared to a living cell, it has a very simple biochemic structure. However, chance of finding RNA fossils are, ehm, like building a 747 by a tornado... out of straws :-)
Stephen J. Gould, the co-author of the "punctuated equilibrium theory", which was supposed to dismiss neodarwinism, had to write a book entitled - I'm translating from polish, don't know the english title - "Darwins too-early funeral". Well, let's see what happens to this theory :->
Regards,
January
[*] Disclaimer: I program in C on an AIX.
Yes, this fellow is most likely completely off his rocker. But let's keep something in mind, all right?
1. This theory depends on DNA/RNA molecules being able to perform quantum computations. If DNA/RNA are not efficient chemical "vehicles" for quantum computation, then this theory is completely and utterly wrong.
2. This theory can actually be proven wrong, unlike almost every other evolutionary theory out there. You name the theory -- Punctuated Equilibrium, Red Queen, Designed Evolution... their mechanisms are all-but-unobservable, and cannot be empirically tested in a lab (as best I know). This theory can be tested in a lab; if DNA/RNA isn't good at quantum computation, presto, the theory's wrong.
3. Don't dismiss it because it didn't appear in a scientific journal. Odds are nobody would touch this one with a ten-foot pole; it's so far from conventional science that it's easy to dismiss it as being crackpot. But this fellow has a serious idea, and he's also conveniently provided us with a way to prove him wrong. Don't write him off as a nut and not worth your time just because he's published in a book -- first prove him wrong, and then write him off as a nut. Not before, and certainly not in the reverse order.
4. Dismiss anyone who says "this man doesn't know a thing about quantum mechanics" just because he takes a weird view of the implications of quantum mechanics. His theory, as best as I can tell, depends on the Everett many-worlds interpretation of quantum mechanics. I prefer the Copenhagen interpretation, but you know what? Neither one of them is in the slightest bit scientific.
Quantum mechanics is a fact. It describes observed phenomena, it has successfully predicted phenomena, and it can be proven wrong (not that it ever has been proven wrong -- but if you were to ever successfully measure both the precise location and velocity of a particle, you'd prove QM to be an incorrect theory). The problem is that quantum mechanics is so alien to our idea of the universe that most physicists have to come up with a framework from which quantum mechanics makes some sort of sense.
This gentleman's interpretation of quantum mechanics is no nuttier than the Copenhagen Interpretation, or even an interpretation that the collective farts of all the universe's sentient races causes the weirdness in QM. Any interpretation of QM is metaphysics, not science. It's easy to say "this guy's a crackpot, since his interpretation isn't shared by any other "serious scientist". It's just as easy, and as accurate, to say "a lot of guys are crackpots because they believe in a multiverse which is constantly splitting off from itself, as proposed by Everett."
For all this fellow's failings, I've got to give him credit for coming up with a perfect theory.
(1) It's insane. As Wolfgang Pauli is supposed to have said to a colleague, "We are all divided on whether or not your theory is crazy. I do not believe it is crazy enough." In QM, crazy is good.
(2) It explains observed phenomena.
(3) It predicts future phenomena.
(4) It's empirically testable.
... In other words, it's a hell of a lot better than most evolutionary theories I've seen. It's probably wrong, of course. But it's wrong to dismiss this one out-of-hand.
I wonder who brought up that dumb argument of Hoyle's -- McFadden or the journalist? The article (and perhaps McFadden) ignores the fact that evolution is guided by natural selection. Complex things like skeletons and brains do not require highly unprobable events in which gazillions of elementary particles glom together at the same instant in just the right way. There is a long sequence of incremental improvements, and the best improvements increase the odds of survival and the odds of the improvement being passed on. Other than the point about cells sometimes appearing to choose advantageous mutations, the article doesn't say why this quantum explanation is needed, or why it explains things better than natural selection. (E.g. another possible explanation of the cells choosing advantageous mutations is that they've evolved to do so.)
"It's too improbable" he says, ignoring the very fact that under the Many Worlds Theory, his ideas and Darwinism are essentially identical.
Then, there's one detail that he conveniently ignores. Biochemistry is VERY SPECIFIC. You can't join any old chemicals together.
DNA, for example, has 4 possible bases. This should give you 16 (4^2) possible combinations. You don't get those. There are 4 ways, and 4 ways alone to join up those 4 pairs. (You can read from either side, so the order is important.)
That reduces the complexity of the system, substantially. In theory, you could read any number of pairs from 1 to infinity, but RNA takes a block of exactly 3. No more, no less.
You see the catch with this whole complexity idea? The fact is, biochemistry is complex through scale, not permutations. The permutations are all dealt with, by the very nature of the system.
In short, biology exists because it removes the complexity at any given level. Each level within the system is extremely simple.
Protein construction involves 1 copy operation (which takes place nearly automatically, via messenger RNA), 3 identical attach operations (which take place without any active participation of the mechanism) and 1 destruction operation of the template. (You really don't want too many templates floating around. Could cause a mess.)
Nothing in there is complicated. The messenger RNA attaches to the DNA. The appropriate chemicals attach to their mirror images on the DNA. (Nothing else -can- attach. It's not possible.) The Messenger RNA, plus template, detatch. Fresh chemicals now attach to the RNA, mirros of the mirror, thus the original sequence. This is your protein. The template is then destroyed, and the process repeats.
What's so complicated about that? All you have there is something that replicates and inverts. Very trivial to construct.
How do you get DNA and RNA in the first place? I imagine the reverse of the current process, almost. Amino acids probably clumped together, onto some simple strand, with related amino acids pairing off. Strands that weakly attached would give you your proto-RNA. Those that bonded more firmly would give you proto-DNA.
In other words, the environment would become one gigantic proto-cell.
Last, but not least, if anyone's read this far, I do have something to say to the God theory. I am Christian, and I believe that life, of all kinds, exists for a reason beyond merely being. However, I do =NOT= subscribe to the theory that we should live in ignorance and fear.
If you read and accept the Bible, whether as literal or moral truth, there are two pertinent ideas that come forward. God created humanity in His image. Humanity is inquisitive, and has always been. Thus, wonder is a part of God's creation. To deny wonder, and worship ignorance is to sin against God, for it is to tell God that His image isn't good enough for you.
The second part is Jesus telling his followers to be like children. "For it is such as these who will enter the Kingdom of Heaven." You find a child who won't ask "WHY?" You find a child who won't question. If questioning, and not blindly accepting an alleged truth which isn't even given =in= the Bible, for all the claims of the allegers, is to enter the Kingdom of God, you'll find more geeks in Heaven than the Christians who aren't.
After all, THEY are the ones who have become like little children, forever questioning. Seeking. Trying things out. Learning.
Those who "know it all", because they claim to be a Christian, are like harsh parents, always critical and condemning. God does, indeed, have a place in mind for those who seek to put themselves above Him. I've heard it's nice and warm there, too.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
1) The real world (whatever that is) is, as far as anyone knows, governed by the laws of Quantum Mechanics. Period. So the question is not the applicability of QM, but of Classical Physics which is an approximation of QM in some circumstances (very large distances scales, energies, quantum numbers etc.). So QM could be used to describe buckyballs -if you could do the calculations- and yield a more accurate answer than CM.
2) Getting closer to the topic, this article smells kind of fishy. McFadden doesn't seem to understand Quantum Mechanics. I know, I know. He claims noone does, and on some fundamental level, that may be true. But we do know how to make some pretty damn precise calculations and predictions with it. Which requires at least some understanding.
For example the claims about an electron going in two (or more)different directions: true, but it's somewhat more complicated than that. If you try to observe an electron doing that, you never will. But if you don't check which way the electron went it can look like it went two ways (you can do a double slit intereference experiment with electrons, to invoke Physics 102- depending on how you do the experiment, you get an intereference pattern or not. With the interefence pattern, that means that the electron went both ways in some sense).
Another example: a particle is always in one and only one state at a time, never billions. However one state (say a state of definite energy) can be thought of -for some purposes- as a combination (superposition) of many other states (say states with definite position). But it is really only in one state.
3) The multiverse interpretation of quantum mechanics is strongly disfavored (though not discredited) by physicists. Primarily because there is no real way of testing or disproving it. It predicts exactly the same things as the "orthodox" (aka Copenhagen) interpretation, which is simpler.
Ok, that's all I have to say for now.
Oh, please don't misunderstand me -- I'm not calling evolutionary science meaningless, or based on shaky foundations. I just draw a line between observed phenomena and hypothetical explanations for those phenomena. I've read plenty of descriptions of evolution in action to believe that it exists; I've yet to read a theory explaining evolution which I feel has a substantial chance of being substantially correct.
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This doesn't mean that the field is useless. Far from it; it means the field is extremely useful, because somewhere there's a whole lot of discoveries just waiting to be made.
I just think we're a long way from having a good theory of how evolution occurs -- that's all.
Insofar as explaining observed pheonomena, predicting future phenomena, empirically testable, I submit the punctuated-equilibrium theory to you. Hypothesizing that evolution happens in times of catastrophic ecological upheaval is all fine and dandy, but it's kind of hard to conduct controlled tests of the same, don't you think?
My own personal belief is that geographic isolation and punctuated equilibrium are, taken together, probably the most promising ideas. The geographic isolation bit you can actually test under reasonably controlled conditions; the ecological catastrophes, less so.
Warning: I am not a biologist. I am a computer scientist. As you can guess, I'm not an expert in the field -- I've read enough to be dangerous and maybe enough to hold an intelligent conversation, but that's all.
$1,040,000,000 for this? News for crackpots, stuff that really doesn't matter at all.
I want something better. I've got the domain "cluedot.{org,net,com}". I've got collaborative filtering technology, implemented on Advogato that might just solve the problem of miniscule S/N ratios. I just don't have the time myself to put it into production right now, as I'm too busy developing free software projects. Anyone?
Yes, yes, I know. Troll, Offtopic, Flamebait, whatever. Karma be damned, I'm pissed off to see a site that used to be my kind of news site indulge in such stupid crap.
LILO boot: linux init=/usr/bin/emacs
"But if everything is True by Decree and questions are met with hostility or silence, then this I believe speaks volumes about the convictions of the religious followers own belief in his system."
Sounds like you haven't met your kind of Christians, yet, actually. Not all Christians react with "hostility or silence" when their beliefs are questioned. There are way too many that do, to be sure, but not all.
Besides, the truth of Christianity can't be proved or disproved by the behavior of those who claim to subscribe to it. If Jesus Christ died and rose from the grave, then he died and rose from the grave, whether or not the people who say they believe in that fact act like idiots or not. I suggest that if you are seriously interested in verifying Christianity that you nose around for yourself. "Evidence That Demands a Verdict" by Josh McDowell is probably a good start. You may be pleasantly surprised.
Alright, here's my take on this. It sounds like there are some problems with neo-Darwinism, but everything is not as bad as you make it sound here. :)
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First, we don't know how old the Earth is, and we don't know how old the Universe is, but we have some pretty good guesses. However, anything in the "thousands" of years is definitely waaay too short, unless you're going for the "everything spontaneously came into existence five minutes ago, complete with false memories" argument, which would mean that I didn't *really* get that A+ in "Philosophy of Science", I just remember it that way.
Second, radiometric dating is pretty accurate and well-verified, provided your timescale is in geological time (which is what matters, for the age of the Earth--we're not trying to compute *my* age here). So an error plus or minus a few thousand years doesn't really matter when your timescale is in the millions or billions of years.
I repeat, don't try to date anything recent, it just doesn't make sense. If you don't believe the earthi is actually that old, do some research on the magnetic properties of rocks and their correlation on the ocean floor (due to the periodic switch in the magnetism of the earth). This is how they found more evidence for continental drift, and there's enough there to make a convincing case for the age of the earth being much greater than thousands of years, and therefore makes a case for the use of radiometric dating as a useful tool (measuring for millions or even billions of years).
Third, a species isn't a hard-and-fast definiton, and it's purely practical. There are sub-species as well. But there are some good guidelines. You should be able to breed within a species, for instance. Some good evidence for differentiation and competition would be, say, Australia. Theoretically, it drifted away from the other continents before the marsupials got out-competed. Therefore, Australia still has marsupials, because they were dominant in a (relatively speaking) small area, and ended up succeeding. Some of the same environmental niches are present, and the marsupials evolved to fill them, just as other animals did on the other continents. Of course, this theory requires continental drift, and geological time, and evolution, etc., etc.
Random beneficial mutations *are* rare. However, selective breeding works pretty well. If a lot of people have a lot of latent genetic traits that aren't used under pressure, and then a disease wipes out a lot of people that didn't have those traits, the people left will breed, and tend to have more of those beneficial traits. Random mutation is all well and good, but diversity in the gene pool over a long period of time seems more helpful to me.
I'm sure there are good explanations for the gap in the fossil record. But in science, just as in religion, we have to go with what we know, and try our best to fill in the gaps. Maybe if we found more fossils, we'd have a more solid theory in that respect.
Or maybe God is just taunting us, eh, just like he taunts those Sunday school kids with "Who did Adam and Eve's children marry", or whatever.
Maybe some neo-darwinists got the speciation tree wrong there, it's something to think about. But snakes, crocodiles, and chickens are all pretty far apart, with snakes being the weirdest. Think about it, they lost their legs a long time ago, whereas crocodiles and chickens walk around just fine. Also, the dinosaurs might have been related to those chickens just as much as they were to the crocodiles, that's also been a recent evolutionary theory. At least there's argument and change happening in this field, that shows that it's alive and well, not dead and buried.
I don't know much about Lamarkian change, probably because it's a pretty lame theory. It seems to me that acquired characteristics couldn't strictly be bred for, which is the flaw in Lamarkian theory. However, individuals who learn how to do these actions might survive better, and teach their young, which would be a valid Darwinian theory.
(say a woman on a desert island learned how to shake coconut trees and get the food out of them. She's smart, she survives, she teaches her children, they survive. More of them survive and breed, and the rest of the island eventually learns the secret and gets smarter.
Fitness shouldn't be defined simply as leaving the most offspring, but that's a good start. Obviously you had to survive to do so, which is the point. Over a long period of time this is a good definition, because the survivors inherit the earth, and everyone else dies out. In that environment, they are fit.
That link you provided cleared things up a bit, thanks. It looks like neo-Darwinism is a specific branch of Darwinism that these people have chosen to attack. Of course, a decent theory would have to be a bit more complex than they have portrayed.
Yes, animals with different DNA can look more similar than animals with the same DNA might appear. (bats and blue whales are both mammals--DNA analysis tells you how long ago a species might have diverged, not what they look like now)
Yes, beneficial changes can happen very quickly. I don't know how that works exactly, but I'd gather it would be a survival trait that can be bred for. In fact, I wonder how many of these survival traits we don't know about. I doubt Luck is one, but that idea figures strongly into the Ringworld books, and even if its wrong, it looks like a good example of thinking outside the box, like the box that web page placed neo-Darwinism into, and definitely not all Darwinistic insights.
To keep coming up with more good theories, there have to be more insights. Followers, by definition, do not have more insights. The only way to get them is to think up something else, and see if it works. Evolution is more complex than Darwin let on, but he didn't finish the job here, he only started it.
If anyone really knowledgable has some insights on either of these topics, please respond.
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pb Reply or e-mail; don't vaguely moderate.
pb Reply or e-mail; don't vaguely moderate.
> No existing religion is willing to continually challenge and dispute itself in this manner.
Au contraire, mon ami. Almost all major religions are consistanty refining and reworking their beliefs to fit new information. Most Christian denominations, for instance, have annual meetings that, among other orders of business, decide on any 'platform' changes or additions. Just like science, some core truths are relatively stable (gravity, the divinity of Christ), some are slowly retired over time (flat earth, flat earth), and some are still in flux (particle physics, the role of women in the church).
Just because religions' criteria for changing truths is not necessarily based on empirical challenging doesn't mean their methods are demonstrably 'wrong.' Unless you're such a believer in the Church of Science's core tenets of demontrability and repeatability that any other scheme is 'heresy.'
>But if everything is True by Decree....
Again, science is a church. Unless you personally go out and demonstrate each and every scientific truth that you believe, for yourself, with strict application of scientific method and a healthy dose of skepticism, a belief in science IS "Truth by Decree," relying on the proclamations of wiser elders for truth, based on a faith in their higher knowledge of and closer contact with The Truth.
"Peer review" isn't an argument against the above, either. Almost all Christian elders, of any denomination and creed, will back each other up on the divinity of Christ, using the tools of their Church. If "peer review" is a criterion for truth, why don't you believe in those alleged truths?
Unless it's that what your argument boils down to is "if it doesn't work the way science says, I won't believe it." Which, to me, sounds like a belief system based in faith.
As a disclaimer, I, myself, am a Church of Science adherant, and not a religious person of any consequence. But I do see that my Church is just a system of ordered beliefs handed down from power structure to power structure, with a core set of unprovable assumptions, occasional attacks from 'fringe breakaway groups' that either succeed or fail, and with millions of amateur adherants that gobble up things that are sound like dogma and pooh-pooh things that don't, with very little except their incomplete understanding and faith to tell the difference. And just like any other Church, science is anxious to differentiate itself from other Churches by argument of how much better and more valid its ideas are.
The fact that the Church of Science has been the in-fashion flavor for the last few hundred years doesn't mean it's any less a Church, no matter how strongly it tries to redefine itself.
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Firstly, I'd like to recommend to you and everyone else that when you read and "earthshattering" book that punches holes in some scientiifc orthodoxy, you go out and check your facts. Mr Milton may be the untold genius of 20th century biology, but its much more likely (especially if you presentation of his arguments is faithful to his) that he's a second rate scientist,or even a simple kook, trying to make a few bucks.
Point by point now ...
Age of the Earth We don't know the age of the earth very precisely, but we have a pretty good idea. You can use rocks to date fossils and fossils to date rocks as long as you don't use the fossils to date the rocks you used to date the fossils. Nothing circular about it. Different radiometric dating techniques are used for different things - carbon dating (used for organic matterto get the date since death) is accurate to the hundreds of years, the techniques used for rocks are only accurate to thousands or millions of years, so using them to date recent lava flows in an exercise in bad science. Can't comment on the stalactites, but off the topof my head, surely it depends on the quantities of water, and the quantity and nature of the minerals dissolved in them. I know of stalactites that have formed in only 10s of years myself.
Definition of Species Species is not an important concepts in neo-darwinism as currently formulated. The only things upon which natural selection works are genes, and the only way in which it does so it through their phenotypic effects. Whether or not speciation has been observed is not terribly relevant - if you accept that the fossil record is an accurate but incomplete record of the earth's biological history, it must have happened. Several phenomena (ring species,evidence for punctuated equilibria in the fossil record) suggest that speciation occurs when a small population is separated from the rest of the species and evolves on a separate track.
Beneficial Mutation is stupendously improbable by ordinary human standards. noone is proposing that large scale evolutionary change occurs of timescalescomprehensible to human intuition. I don't know what the stuff about directed mutation is on about. If you have references I'd be interested.
Punctuated Equilibria isnot an ad-hoc explanation for anything. The absence of link fossils is explained quite sufficiently by the extreme rarity of fossilisation. Punctuated equilibria is just a theory about what happens during speciation and what we should expect to see in the fossils record in any given location -the interesting point being that if speciation really does usually occur in isolated populations, we should not expect to find link fossils in the same place as the parent and child species,even if all individuals were fossilised.
Haeomoglobin I've no idea how the quoteyou give is supposed to shed doubt on the idea that "DNA determines the characteristics of the organism". Taken literally, noone believes that anyway. Many other factors play a role.You can't taken cheicken DNA and magically produce a chickenfrom inorganic matter. Regardless, we're presumably meant to conclude from the quote than chickens are in fact more closely related to both snakes and crocodiles than they areto one another,or that common DNA is not a good measure of relatedness. Either is fine - neither is a blow to the neo-darwinian synthesis. Whether snakes and crocodiles are both reptiles is irrelevant - this taxonmic distinction has no bearing on anything else, least of closeness of relatedness. Similarly evolutionary forces may have acted on one or more of the three creatures to change the shape ofits haemoglobin.
Lamarkian Change Larmarkism is not a well formulated theory. Some darwinian change could be classified as Lamarkian.
Natural selection is not a tautology. The statement you make is a tautology, but is only half the story. Properly stated, the principle of natural selection is something like "those genes whose phenotypic effects cause creatures carrying them to tend to survive will spread through the population". This is not a terribly complcated concept, but it is not a tautology. The idea that this is the main driver behind evolutionary change is another matter -by and large this is believed because noone has proposed a more credible theory.
Greenrd dun said:
In a word--Duh. For many reasons, at that.
First off, fifteen years ago, genetic cladograms were in their infancy.
Secondly, a good deal of what we now know about "reptilian" evolution has come about literally in the past fifteen to twenty years. (We have literally gone in twenty-five years from thinking dinosaurs were slow, cold-blooded creatures to realising that birds (which are among the hottest- blooded critters there are--sparrows typically have a normal body temperature of around 110 degrees Fahrenheit, or around 42 degrees C) are in fact theropod dinosaurs.) This has been both through genetic cladograms AND by fossil remains--much of the fossils that have shaped our present view of dinosaurs, in fact, have come up literally within the past five to ten years, and some of the most astounding yet (feathered dinosaurs, and many fossils that pretty much trace the entire history of how dinosaurs developed powered flight, along with typical "avian" traits like feathers, brooding eggs, even when hard-shelled eggs may have developed) have literally only come to light in the past two years).
Thirdly, I have my doubts that, even fifteen years ago, scientists thought crocs were closer to snakes than birds. (Just some info for you--on occasion, people who are trying to debunk evolution have been known to outright tell porkies. I've seen this far more often with "Creation Science" groups funded by fundamentalist "Christian" groups here in the States, but I wouldn't put it past some newage (rhymes with sewage) groups, either. And from what I've read, this sounds really suspiciously like newage (rhymes with sewage). In other words, don't trust everything you read--verify first. :)
The reason I doubt that they thought snakes and crocs were closer than crocs and birds is because it has been known for at least the past fifteen or so years that birds and crocodiles were part of a group called the Archosauria. (Archosauria, for your information, is a clade that is considered roughly equal to the old "Reptilia"--Reptilia has actually been split. Archosauria contains thecodonts, pterosaurs, dinosaurs, and crocodilians (note I've not expressly mentioned birds--I'm going to get to that). Just FWIW.) Snakes have, for at least the past twenty years or so, been considered to have evolved from lizards; there is a controversial theory that snakes instead evolved from mosasaurs, but mosasaurs are still not terribly related to archosaurs (they instead form yet another sister clade) so the point still stands.
Anyone who had the faintest idea about paleontology--who had so much as kept up with some of the early writing on Deinonychus or read a copy of Robert Bakker's "The Dinosaur Heresies" (written in 1986, talking about the "hot theories" already circulating in paleontology--many of the "heresies" have been recently vindicated, btw)-- would bloody well know crocs are closer to birds than snakes, unless he didn't keep up with paleontology at all. (It is entirely possible they didn't. As late as the early 1990's people were still being taught about "slow, sluggish, cold-blooded, naked-skinned" dinosaurs.)
For the record, especially in the field of dinosaur paleontology, fifteen years is damned near an eternity nowadays. Among other things, we've found evidence that the closest relative of Deinonychus (the one dinosaur that, along with Archaeopteryx and now the feathered dinos coming out of China--yes, you heard right, feathered dinosaurs--gave paleontology a needed boot in the arse with its sickle-clawed feets) is in fact Archaeopteryx, the first bird; that dinosaurs cared for their young (this has now been documented from "duckbilled" dinosaurs all the way to Tyrannosaurus rex itself--a juvenile named "Tinker" has recently been found, which has been teaching a lot on both juvenile tyrannosaurs and tyrannosaur family life) and that theropods even brooded young like chickens or ostriches (at least two oviraptor fossils have been found brooding nests); there have been incredible fossils as of late coming out of China which include the first feathered non-avian dinosaurs; we now have a large number of transitional fossils documenting nearly the entire evolution of flight in dinosaurs (from pre-avian feathered dinos, including display feathers on arms and tail, to Archie, to development of the alula feather from the thumb); we have entire evolutionary sequences for many families of archosaurs (including dinosaurs and crocs--we now know early crocs were ground-runners and that crocs are actually incredibly derived archosaurs); we even now have evidence that some dinosaurs like (oddly enough) Deinonychus may well have evolved from early protobirds and become secondarily flightless. Paleontology has come by INCREDIBLE leaps and bounds; one might say the science fifteen years ago was in prehistory (pun intended).
Oh, among things (both from re-analysis of fossils and new finds, and from some genetic studies including embryology studies) relating to the little comparison: Reptilia has now been split into the four groups other than archosaurs (ichthyosaurs, lizards/snakes, tuataras, and turtles), and Archosauria is now class-status. Crocodiles' and birds' last common ancestor was approximately 225-200 million years ago, when basal thecodonts split into "arctotarsal" and "crurotarsal" lineages (this is denoting ankle structures--one can say "bird-ankled" and "croc-ankled". Around the end of the Triassic, crocs evolved from "croc-ankled" thecodonts as ground-runners; they then proceeded to specialise as water-hunters, including specialisations in the heart for suspended animation underwater, etc. (Croc hearts are supposedly some of the most derived in the animal kingdom.) Dinosaurs evolved at around the same time from "bird-ankled" thecodonts, probably little ones like Lagosuchus; birds are now recognised (after a hell of a lot of evidence, and finally a few clue-by-fours out of Liaoning, China that finally settled many questions of dinosaur and "bird" evolution) as being a surviving group of theropod dinosaurs (specifically, maniraptorian neotheropod theropod dinosaurs) that survived the K-T boundary (there is about as much link between dinosaurs and birds as there is between mammals and bats; birds are dinosaurs and always have been, and most paleontologists have sunk Aves into a subgroup of dinosaurs at best and usually down to a theropodian subgroup--you will actually hear discussions of "neornithian dinosaurs").
Oh, and for the record--the same shakeup in cladistics that has led to birds being finally recognised as dinosaurs has also removed "mammal-like reptiles" from Reptilia and put them in a group with mammals and therapsids (therapsids are basically proto-mammals; they're related to us in the same way that early dinosaurs like herrerasaurs or dilophosaurs are related to birds). Yes, Mammilia got sunk in the process, though not as badly as Aves has.
In other words, the genetic cladogram actually proved RIGHT (dinosaurs and crocs are, in fact, archosaurs which derived from thecodont lineages that split fairly early in archosaurian evolution). Which blows hell out of the argument. :)
Oh, another fun fact--the same genetic cladograms also show that chimpanzees, bonobos, and humans are literally more closely related to each other than to any of the other great apes (they also led to gibbons possibly losing their status as a great ape). Chimps and humans share around 98 percent of their DNA, and bonobos are even closer if memory serves. It is probably a matter of a few evolutionary changes and some reordering on chromosomes that differenciates Homo sapiens from Pan paniscus (the bonobo, the closest living relative to humans and not terribly far from australopithecines--they have been known to make tools and they do walk erect fairly often).
As for other arguments:
On the age of the earth: Most of what we know is based on dating of rocks here and in other parts of the solar system. For the oldest rocks on Earth we have a lower limit of around 3 1/2 billion years (this is based on radioactive decay halflives, which have been proven sound both mathematically and experimentally--if there is funkiness with radioactive decay, I'd suggest you share it now :). Both strata-dating AND radio-dating are used, as checks on each other (especially when you are dealing with very old rocks where there are no diagnostic fossils that can date the rock).
We've also got rocks from other parts of the solar system (most notably meteorites [some of possible Martian origin] and moon-rocks). These have likewise been radio-dated, and give an upper bound of around 4 1/2-5 billion years. (Rocks from Earth don't exist from then because Earth was essentially a big ball of cooling lava at that point. :) So between the two, we can safely state the Earth is probably around 4 1/2 billion years old, give or take a few million years. (FWIW, this has also been checked by extrapolating and finding the age of our Sun based on the millions of stars we've observed--we know pretty much how baby stars are born and grow and die, and how stars of the mass of our Sun tend to behave. Also, for really old rocks, one of the dating methods uses uranium--uranium has a half-life of some six billion years in its most stable isotopes, which is just about right for measuring the age of a solar system.)
On species: Actually, yes, there is a specific definition of species both for fossil remains and for living specimens--there is actually a specific convention of species nomenclature called the ICZN, or "International Convention on Zoological Nomenclature". Summed up:
Living Species/Non-Fossil Remains: Species is defined as when two members of a population have diverged genetically to the point that they cannot easily interbreed. (Incidentially--it is this very definition of species that caused both dogs AND cats to be sunk into subspecies. Until 1994 or so, dogs were officially listed as Canis familiaris and cats as Felis catus; recent genetic studies have shown that dogs and cats ARE genetically still wolves and African wildcats respectively (just with a lot of the natural genetic variation brought out by selective breeding)--hence dogs are now Canis lupus familiaris and cats are now Felis sylvestris domestica. For that matter, there's been a lot of DNA testing of Neandertal remains to see if we can find out whether we could have interbred with them--if it turns out Neandertals and modern humans could interbreed, Neandertals are just a subspecies of us (Homo sapiens neandertalensis) but if we couldn't, they get their own species name (Homo neandertalensis).
In fossil species: Species is defined as such point as a morphological change has occured in a fossil specimen as to distinguish it from other existing fossils that may be of that type. (Since in most cases genetic studies cannot be done of fossil remains, they basically go by "has there been a major or minor change in this organism". Most fossil classifications beyond the genus level tend to be controversial unless there is good evidence to account for them, both in morphology and (on occasion) in habitat (such occurs in the two species of tyrannosaurs, Tyrannosaurus rex and Tyrannosaurus bataar--bataar is smaller than T. rex, and T. bataar is found in Mongolia where T. rex is found in Montana and western North America).
On random mutations: Actually, random mutations can sometimes be beneficial--and sometimes even both. A good example is with some genetic diseases such as Tay-Sach's Disease (nearly always fatal before 5), thalassemia, sickle-cell anemia, and cystic fibrosis (all three of which are debilitating and potentially fatal)-- as it turns out, two copies are Bad, but having one copy actually protects you against some other disease (with Tay-Sachs, it's tuberculosis [which was very common in ghettos, where Ashkenazi Jews (the major carriers) lived]; with both thalassemia and sickle-cell anemia, one copy protects you against malaria (the genes evolved separately in the Mediterranean and Sub-Saharan Africa, and there are other sickling/"deformed" genetic diseases of red blood cells that have the same protective effect against malaria in small doses in Southeast Asian populations); one copy of the cystic fibrosis gene is protective against cholera (in fact, what goes wrong in cystic fibrosis is now known on a chemical basis as a defect in chloride excretion--as it turns out, the exact opposite disorder occurs in cholera! One stops you up, the other gives you the raging squits...). Even though these genes cause bad (sometimes tragic) effects in double-doses, they actually are beneficial enough that they've stayed in the human genome for thousands of years (unlike most genetic diseases with no good benefit, which generally only tend to show up when people end up marrying cousins or people get seriously inbred).
Also, sometimes it doesn't take a HUGE mutation. The length in arms of Archaeopteryx really is not that much longer (per body ratio) than that of Deinonychus (much bigger, non-flying, but skeletally very, very similar to Archie). If there is something to work with, it can give an animal an advantage. Said animal does the nasty, passes their genes along, and if it's good it spreads. (BTW, the fact that humans and chimps share 98% of DNA and have about as much difference both in actual gene content and chromosome-count as horses and donkeys do (humans have 46 chromosomes--chimps have 48) show that it does not take a terrible amount of mutation to evolve.
Also, sometimes it's not so much a matter of evolving new things as "sports" showing up with OLD traits that prove useful. Phorusracid birds, which evolved tens of millions of years AFTER non-avian dinosaurs went extinct, actually redeveloped flexible fingers with claws--a trait that had laid dormant in birds since the late Cretaceous--and adopted a ground-running hunter lifestyle, like nonavian theropod dinosaurs, which was very successful for millions of years (mammilian predators of megafauna finally did them in anywhere from 2 million to 750,000 years ago, but until then they were the top predator niche in South America). Hoatzins have claws when babies which is a reversion. Chickens are on occasion born with teeth (this too is an old archosaurian trait).
On punctuated equillibrium: Actually, there are cases where it does occur. One of the biggies seems to be powered flight (flight is incredibly advantageous, and is usually refined very quickly after invented). And even in that case we DO have "missing links"--plenty of them. Hell, with dinosaurs we have an almost 100-million-year-old continuous string of evolution showing from early protofeathers (Sinosauropteryx) to examples of display feathers on tail and arms (Caudipteryx) to possible pre-flyers or very early flyers (Protoarchaeopteryx) to full-fledged flyers (Archaeopteryx) to more advanced flight (fossils from China showing development of alula feather from clawed thumb) to advanced toothed forms (birds like Hesperornis) to paleornithe birds to the beginnings of a lineage of extant modern birds (chadriiforme ducks) to an actual reversion towards an older condition (phorusracids) to now. Also, around the time of Archaeopteryx we may well have a complete record (including many transitionals) of both an initial radiation of sickle-clawed early "birds" and (most tantalizing) either the co-evolution of archaeopterygids and dromaeosaurs as sister species or possibly dromaeosaurs outright evolving from archaeopterygids. (The latter would REALLY be something, and a fair amount of evidence IS pointing that way. Don't be surprised if you hear around two or three years down the road that Deinonychus is probably secondarily flightless.)
A more classic evolutionary sequence (with tons and tons and tons of transitional fossils) is the sequence of horse evolution.
-Windigo The Feral (NYAR!)