The Case for Macroevolution

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ʝօɦռ 6IX ɮʀɛɛʐʏ's picture
What do you get when you

What do you get when you crossbreed a Greensnake and Sushisnake?

Sushisnake 's picture
Probably a scaleless

Probably a scaleless freshwater snake with barbels.

Qu@si's picture
"What do you get when you

"What do you get when you crossbreed a Greensnake and Sushisnake?"

hhmmm...you'll get a more rational and more honest than you john...that's all i can predict..

sorry that's the fact..

aperez241's picture
I like them too. Water bears

I like them too. Water bears are cool..!

Sheldon's picture
"Evolution needs life to

"Evolution needs life to originate by natural processes,"

What objective evidence can you demonstrate for any "other" processes?

You're trying to misrepresent the scientific fact of evolution, and are using argumentum ad ignorantiam to insert a deity and magic into a gap in our knowledge for how life originated. Dear oh dear John, how long can you maintain the pretence of being a scientific genius whilst denying scientific facts, and championing superstitious beliefs about magic.

Greensnake's picture
John 61X Breezy,

John 61X Breezy,

Evolution is written in the fossil record, in the data of comparative DNA, and in all of the other data given by Dr. Theobald in his outline. Do you think all that's going to disappear if some divine agent was responsible for the first reproducing cell? Wake up and smell the coffee!

If a geologist sees a path that indicated that a great boulder had rolled down the hill, is that historical reconstruction going to change if it were discovered that someone gave that boulder a push instead of natural forces acting on it? Think about it.

ʝօɦռ 6IX ɮʀɛɛʐʏ's picture
Take a walk down the history

Take a walk down the history of science. You'll often find that new paradigms don't just bring new ideas, they bring new interpretation to all the previous observations. You can always connect the same dots in different patterns.

Sheldon's picture
Since when is a 2 to 3

Since when is a 2 to 3 thousand year old religious superstition a "new scientific paradigm"?

What process is validating this superstitious creation myth, and the unexplained magic it uses?

Greensnake's picture
John 61X Breezy,

John 61X Breezy,

Another diversion! How about replying to my post, directly and to the point?

Greensnake's picture
John 61X Breezy,

John 61X Breezy,

Paradigms may change but the facts don't. The conclusions of abiogenesis have no effect on the facts on which evolution is built. Neither the facts of the fossil record, or of the DNA relationships, or of cladistics, is affected by any conclusion reached by abiogenesis. The fossils don't leap into new orders! Comparative DNA data doesn't reshuffle their relationships! If you still can't understand something this basic, then I can't help you. But I can ignore silly evolutions of this argument and save myself some time.

Nyarlathotep's picture
Scott242 - First of all, as

Scott242 - First of all, as Perry Marshall points out in his book Evolution 2.0, it is possible to prove that a pattern is non-random, but there is no mathematical procedure for proving that a pattern is random. Atheists can only assume that genes mutate randomly…because their worldview demands it. But the random mutation hypothesis can never be verified, and therefore it stands in opposition to the scientific method itself.

How exactly does Mr. Marshall prove that a source of numbers is not random?

Also hypotheses in science are never verified with proof; so it seems like you have created an infinitely high bar for something to pass over, then claim victory when it can't pass it. That sure seems like some dirty pool.

Scott242's picture
Nyarlathotep,

Nyarlathotep,

Demonstrating non-randomness clearly lies within the scope of science. For example, SETI (the Search for Extra-Terrestrial Intelligence) considers a string of prime numbers received in a radio signal from space to be a clear indicator of intelligence. The famous atheist astronomer Carl Sagan acknowledged this.

But although non-randomness can be scientifically verified, randomness cannot. Therefore, the randomness of Darwinian revolution will always remain an atheistic philosophical add-on to Darwinian theory, and not science.

Furthermore, both everyday experience and information science tell us that codified information can only be produced by an intelligent agent. In his book Evolution 2.0, Perry Marshall explains the scientific reasons why DNA is a language in the most literal sense. This is not some “loosey-goosey analogy,” as he puts it:

Rutgers University professor Sungchul Ji’s excellent paper “The Linguistics of DNA: Words, Sentences, Grammar, Phonetics, and Semantics” starts off, “Biologic systems and processes cannot be fully accounted for in terms of the principles and laws of physics and chemistry alone, but they require in addition the principles of semiotics— the science of symbols and signs, including linguistics.”

Ji identifies 13 characteristics of human language. DNA shares 10 of them. Cells edit DNA. They also communicate with each other and literally speak a language he called “cellese,” described as “a self-organizing system of molecules, some of which encode, act as signs for, or trigger, gene-directed cell processes.”

This comparison between cell language and human language is not a loosey-goosey analogy; it’s formal and literal. Human language and cell language both employ multilayered symbols. Dr. Ji explains this similarity in his paper: “Bacterial chemical conversations also include assignment of contextual meaning to words and sentences (semantic) and conduction of dialogue (pragmatic)— the fundamental aspects of linguistic communication.” This is true of genetic material. Signals between cells do this as well.

See Ji's paper here: https://nyaspubs.onlinelibrary.wiley.com/doi/abs/10.1111/j.1749-6632.199...

Atheism relies on mindless chemical and physical processes to explain life. But the insurmountable problem for atheism is that such mindless processes can never account for the fact that DNA is a language which utilizes the arrangement of symbols…just like a human language. Much as the chemistry of the ink and paper that constitute a newspaper cannot explain the arrangement of the letters in the words of a newspaper, the chemistry of a DNA molecule cannot explain the arrangement of letters in a DNA molecule. Michael Polanyi, a former Chairman of Physical Chemistry at the University of Manchester (UK), who was famous for his important theoretical contributions to physical chemistry, emphasizes this point:

“As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of occurrence of any particular sequence and thereby enables it to have meaning–a meaning that has a mathematically determinate information content.”

It would be just as absurd to assert that mindless chemical or physical processes could write a newspaper article as it would be to assert that such processes could produce a DNA sequence.

Again, the arrangement of symbols (such as letters) according to a language is not something that can be accomplished, even in principle, by unintelligent chemical or physical processes. Werner Gitt is a former Director and Professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig) and former head of the Department of Information Technology. In his book Without Excuse, he discusses the substitutive function of what he terms “Universal Information “(UI):

“Universal Information is always an abstract representation of some other existing entity. Universal Information is never the item (object) or the fact (event, idea) itself but rather the coded symbols serve as a substitute for the entities that are being represented. Different languages often use different sets of symbols and usually different symbol sequences to represent the same material object or concept. Consider the following examples:”

“-the words in a newspaper, consisting of a sequence of letters, substitute for an event that happened at an earlier time and in some other place,”

“-the words in a novel, consisting of sequences of letters, substitute for characters and their actions,”

“-the notes of a musical score substitute for music that will be played later on musical instruments,”

“-the chemical formula for benzene substitutes for the toxic liquid that is kept in a flask in a chemistry laboratory,”

“-the genetic codons (three-letter words) of the DNA molecule substitute for specific amino acids that are bonded together in a specific sequence to form a protein.”

The substitutive function of the the symbols in a code or language is something that can only be set up by the activity of a conscious and intelligent mind. Physicist and information scientist Hubert Yockey echoes Gitt's crucial point in the primary text on the application of algorithmic information theory to the question of the origin of life, titled Information Theory, Evolution, and the Origin of Life:

"The messages conveyed by sequences of symbols sent through a communication system generally have meaning (otherwise, why are we sending them?)."

"It often is overlooked that the meaning of a sequence of letters, if any, is arbitrary. It is determined by the natural language and is not a property of the letters or their arrangement. For example, the English word 'hell' means 'bright' in German, 'fern' means 'far,' 'gift' means 'poison,' 'bald' means 'soon,' 'Boot' means 'boat,' and 'singe' means 'sing.' In French 'pain' means 'bread,' 'ballot' means a 'bundle,' 'coin' means a 'corner or a wedge,' 'chair' means 'flesh,' 'cent' means 'hundred, 'son' means 'his,' 'tire' means a 'pull,' and 'ton' means 'your.'"

"In French, the English word 'main' means 'hand,' 'sale' means 'dirty.' French-speaking visitors to English-speaking countries will be astonished at department stores having a 'Sale' and especially if it is the 'Main Sale.' This confusion of meaning goes as far as sentences. For example, '0 singe fort' has no meaning in English, although each is an English word, yet in German it means '0 sing on,' and in French it means '0 strong monkey.'"

Simply put, what a symbol serves to represent must be decided upon by a conscious and intelligent agent. Symbolic representation is BY NECESSITY a mental process. Biologists with less rigid ideological commitments to atheism (or at least more intellectual integrity) have been frank enough to admit the necessity of mind (a conscious and intelligent agent) in the origin of life. The Nobel Prize winning Harvard University biologist George Wald, although certainly not an ideological ally of theism, stated the following in his address to the Quantum Biology Symposium titled Life and Mind in the Universe:

“It has occurred to me lately—I must confess with some shock at first to my scientific sensibilities—that both questions [the origin of mind and the origin of life from nonliving matter] might be brought into some degree of congruence. This is with the assumption that mind, rather than emerging as a late outgrowth in the evolution of life, has existed always as the matrix, the source and condition of physical reality—the stuff of which physical reality is composed is mind-stuff. It is mind that has composed a physical universe that breeds life and so eventually evolves creatures that know and create: science-, art-, and technology-making animals.”

See Wald's paper here: https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.560260703

DNA is a language (because it utilizes abstract, substitutive, symbolic representation) that is very similar to a computer language. Microsoft founder Bill Gates writes:

“Human DNA is like a computer program but far, far more advanced than any we’ve ever created.”

Natural processes do not create anything even vaguely resembling a computer program.

Even the world’s most outspoken atheist, the biologist Richard Dawkins, concedes that DNA is a language very similar to a computer language. In his book River Out of Eden: A Darwinian View of Life, Dawkins writes:

“…The machine code of the genes is uncannily computer-like. Apart from differences in jargon, the pages of a molecular biology journal might be interchanged with those of a computer engineering journal.”

Elsewhere, Dawkins writes:

“What has happened is that genetics has become a branch of information technology. The genetic code is truly digital, in exactly the same sense as computer codes. This is not some vague analogy, it is the literal truth.”

Interestingly enough, in an interview, Dawkins concedes that a designer may be behind the origin of life. It is just that the designer Dawkins is talking about is space aliens, rather than God.

Please watch the following video clip in which Dawkins endorses the aliens-brought-life-to-earth-in-their-spaceship hypothesis (known as "directed panspermia") in an interview:

https://www.youtube.com/watch?v=BoncJBrrdQ8&t=1s

Here are Dawkins’ words from the above video:

“It could be that at some earlier time somewhere in the universe a civilization evolved by probably some Darwinian means to a very very high level of technology and designed a form of life that they seeded onto perhaps this planet. Now that is a possibility, and an intriguing possibility…and I suppose its possible that you might find evidence for that if you look at the details of biochemistry and molecular biology. You might find a signature of some sort of designer….”

Sushisnake 's picture
@Scott242

@Scott242

Re: " Therefore, the randomness of Darwinian revolution will always remain an atheistic philosophical add-on to Darwinian theory, and not science."

Natural selection ISN'T random.

https://evolution.berkeley.edu/evolibrary/article/misconcep_05

Re: "This comparison between cell language and human language is not a loosey-goosey analogy; it’s formal and literal."

Human language evolves, too. This is Beowulf in the original Old English:

Hwæt! Wē Gār-Dena in geārdagum,
þēodcyninga þrym gefrūnon,
hū ðā æþelingas ellen fremedon.
Oft Scyld Scēfing sceaþena þrēatum,
monegum mǣgþum, meodosetla oftēah,
egsode eorlas. Syððan ǣrest wearð
fēasceaft funden, hē þæs frōfre gebād,
wēox under wolcnum, weorðmyndum þāh,
oðþæt him ǣghwylc þāra ymbsittendra
ofer hronrāde hȳran scolde,
gomban gyldan. Þæt wæs gōd cyning!

And this is the first four lines of Chaucer's Canterbury Tales, in the original Middle English- London dialect:

Whan that Aprill with his shoures soote
The droghte of March hath perced to the roote,
And bathed every veyne in swich licour
Of which vertu engendred is the flour;

https://en.m.wikipedia.org/wiki/History_of_English

http://www.sciencemag.org/news/2017/11/how-english-language-has-evolved-...
https://ideas.ted.com/20-words-that-once-meant-something-very-different/

Drudger1's picture
Sushisnake,

[copyrighted material removed, Drudger1 is a sock puppet of Scott242, and has been removed --Nyarlathotep]

Sushisnake 's picture
@Drudger1

@Drudger1

Re: "Correct, evolution ISN'T random. Therefore, how does one use evolution as a rationalization for atheism? This is unclear."

I'm not surprised it's unclear to you, since your question is a strawman. NOBODY uses evolution as a rationalisation for atheism. Atheism simply means a lack of belief in god/s. In fact, most theists also accept evolution as fact, not just atheists. Creationists are a tiny, tiny minority of First World believers- largely found in the USA.

I find most people start the way they intend to finish, and since you started with a logical fallacy I confess I didn't bother reading the rest of your long post. Sorry about that. A quick glance told me there were lots of dubious appeals to authority and copious quote mining.

I'm sure one of the other forum members will be along shortly- one who's feeling more patient with fallacies than I am right now.

Nyarlathotep's picture
Scott242 - Demonstrating non

Scott242 - Demonstrating non-randomness clearly lies within the scope of science.

Scott, you said it could be proved. Again, I ask how can it be proved; because if you tell me I will publish that shit right away, because currently there is no known way to do so.
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Think about it:

Would it be possible to get the number 1, five times in a row out of a random generator (1, 1, 1, 1, 1)? Yes.

Would it be possible to get the number 1, five times in a row out of a non random generator (1, 1, 1, 1, 1)? Yes.

So how on Earth, given only those lists of numbers (or any other list) can you prove that one of them is random? You told us it can be done; I'd like to know how.

CyberLN's picture
Scott242, you wrote, “Atheism

Scott242, you wrote, “Atheism relies on mindless chemical and physical processes to explain life.”

FFS, Scott, atheism does no such thing. It is non-theism. That’s all.

You bring up Dawkins, calling him “the world’s most outspoken atheist.” When Dawkins speaks about DNA, he does so as a scientist, an expert in the field. When he speaks about science, he is not reciting any sort of atheist canon.

It seems you want to fuse atheism and science into a single thing. That’s just silliness.

Sheldon's picture
"It seems you want to fuse

"It seems you want to fuse atheism and science into a single thing. That’s just silliness."

But only when it refutes his creationist myth you'll have noticed. Just as Breezy wants us to seriously accept a scientific consensus is worthless, but only so he can deny the one that validates evolution which again......wait for it.....refute his creationist myth.

and around and around we go...

Scott242's picture
Sheldon,

Sheldon,

[copyrighted, spam, removed by Nyarlathotep: you can read it here]

Scott242's picture
CyberLN,

[more copyrighted, spam, removed by Nyarlathotep]

Greensnake's picture
Scott242,

Scott242,

Due to the extreme length of your post, I'll just comment on a few things that caught my eye and can be addressed in a reasonable length of time.

Evolution is based on non-random principles acting in an environment that has effectively random components. This is the nature of evolution--not added on philosophy! As an atheist who is very familiar with the arguments against theism, I would not use evolution for the simple fact that it is not an atheistic argument.

Your whole argument relating to language is based on your own non-expert interpretations of a complex area and uses an authority figure in lieu of arguments. There is nothing clear about it. If you are trying to say that the information in DNA could not have arisen naturally, then I strongly disagree. DNA has a great deal of evolutionary junk in it and actually shows some signs of evolution in itself.

I notice that you do a lot of quote mining. This is not a substitute for arguments and facts. One might disagree with some of your authorities by citing other authorities. Quotes can be cherry-picked, consciously or unconsciously. Statements in a field that you do not understand can easily be misunderstood as I pointed out elsewhere.

Having read some of Dawkins' books and listened to one of his lectures, and having an understanding of evolution, it is pretty clear to me that when Dawkins speaks about "design" he is referring to the "design" conferred by natural selection. Any talk about aliens is most likely a hypothetical point brought up for completeness. I doubt very much that Dawkins believes that life on earth was designed by aliens or anything else. Therefore, you need to drop your claim that Dawkins supported designed life.

It seems that you have also strayed from the topic. We were talking about how well the fossil record supported macroevolution! Unlike Mr. Breezy, who refuses to even discuss the fossil record, you do recognize that it proves that life has changed over time. Do you know of any scientific model other than evolution that can account for the patterns in the fossil record?

Scott242's picture
Greensnake,

[more copyrighted, spam, removed by Nyarlathotep]

aperez241's picture
Genetic algorithms are

Genetic algorithms are programs that evolve and improve based on their previous outcomes. Sometimes they become so complex than their makers cannot guess what they are doing. The changes they go through are random but only the ones that better approach the desired result are kept. So randomness, together with a selective pressure can modify and create a lot of complexity and efficiency in a program without any intelligent intervention. That is what happened through millions of years with DNA.

(edited to correct mising words)

Now, the whole point that we might not know how the DNA came to do not mean that it was designed by any intelligence. All of the DNA reactions are straightforward chemical processes that are very well studied with no magic at all involved.

Scott242's picture
Aparez241,

[more copyrighted, spam, removed by Nyarlathotep, Scott has left the building]

Sushisnake 's picture
Re: " Scott has left the

Re: " Scott has left the building"

Probably a good thing. Poor old Lyn Margulis was probably spinning in her grave at being a Creationist's poster child.

Edit: It's a shame though. I for one get something out of intelligent Creationists coming on and giving us little snippets of the evidence their community is basing its objections on: Lyn Margulis said this; Susan Mazur wrote that, Dawkins used this metaphor and Francis Crick did, too. It's useful, because I end up learning about the actual debates over mechanisms and timescales taking place within the evolutionary sciences ( the ones that have nothing to do with Creationism or its alter ego in drag- ID) and I probably wouldn't know about the debates at all if Creationists didn't cling to them like shipwrecked men cling to flotsam.

Scott actually came within an inch of stating the evidence for evolution is deliberately falsified by science. Fascinating. My jaw dropped.

So it's down to you again, John Breezy. Could be a long wait before another intelligent Creationist turns up because you guys are in a tiny minority. Most Creationists/IDers only offer the Bible or their own ignorance/incredulity as evidence for their beliefs. I really appreciate being able to discuss it with an intelligent Creationist and wish there were more of them around.

Greensnake's picture
aperez241,

aperez241,

It seems to me that genetic algorithms make use of the same principles as does natural selection! In the case of evolution, Mother Nature does the programming. The genes are reshuffled in each generation to produce variations in offspring, and there are many more offspring than can survive. (The resources are quickly exhausted.) The local environment "prunes" those less able to meet the environmental challenges. The survivors then compete against themselves in the next generation. Thus, life becomes better and better adapted under stable environments. This is natural selection in operation.

Whereas natural selection is a case of the environment "deciding" who survives, in artificial selection (plant and animal breeding) humans set the goals. The goal may be fatter cattle, a good hunting dog, a tiny, raggedly poodle, or pigeons sporting exotic craziness. Artificial selection works much faster than natural selection because of human efficiency in mating promising stock and quickly eliminating all others from that gene pool. Thus, evolution (via artificial selection) is rapid. We have, for instance, produced all kinds of dogs sporting huge differences in only a few thousand years! We have produced huge ears of corn on the cob from an ancestor that didn't even have a cob!

Now we have genetic algorithms that take these same, basic principles underlying natural selection and artificial selection and put them into a computer. The programmer, however, has to be clever enough to simulate the production of "offspring" with variations, which "mate" to produce the next generation. As in artificial selection, the human programmer decides which "individuals" of each generation "survive." That is, the program has to make "evolution" work in an abstract sense that has nothing to do with life. That these basic principles of natural selection, abstracted for the computer, do work can be found in the complex circuit design of a computer's central processing units. The task of getting maximum efficiency and speed has long ago eclipsed even the most brilliant engineers working alone or in groups. Every time you turn on your computer, you are benefiting from the power of genetic algorithms! And, it's not just computer chips. Aircraft pushing "beyond" known engineering limits, "impossible" routing problems, and many more complex tasks are now routinely tackled by way of genetic algorithms. And, they are based primarily on the same basic principles of natural selection.

Well, if such wonders can be accomplished by genetic algorithms, what might nature do with those same principles given a couple of billion years or so? The same basic principles that work so well for breeders, and for engineers (as genetic algorithms), could hardly fail for nature given geologic time and the variety of environments. One need only look at the fossil record which, apparently, has totally intimidated Mr. Breezy!

Sheldon's picture
It's been two days and no

It's been two days and no answers so I'm going to repeat my question to Breezy...

Breezy: "Ok, let's do it. Find me such an example of me giving myself a pass, and I'll match it by giving him the same benefit."

Well lets see how many times you have ignored the interrogation you claim others deserve...

1) How many experts on evolution have you shared your creationist ideas with?
2) How many scientific facts do you deny that in no way refute any part of your religious beliefs?
3) How many website with expertise on evolution have you voiced your creationist ideas on?
4) Why are you on an atheist chat room making claims that deny a scientific fact, which just happens to refute your religion's creation myth? There must be cites with experts in evolution after all.
5) Why did you claim the bible denounced slavery but refuse to discuss any texts that actually mentioned slavery?
6) How many of your professors have you shared your creationist denials of evolution with, and what are their qualifications in evolution, and what were their reactions?
7) How many of the scientific texts you have quoted as supporting your claims, don't accept species evolution as a valid scientific theory / fact? Citations please...

Let the evasion commence...

Sheldon's picture
Next time John lol's at the

Next time John lol's at the idea he's giving himself a pass can someone re-post those questions, we wouldn't him crying that I'm spamming again, when the truth is he is relentlessly refusing to answer any salient questions.

Sheldon's picture
Come on John http://www

Come on John http://www.atheistrepublic.com/forums/debate-room/case-macroevolution?pa...

tempus fugit, you've had 4 days after all.

Greensnake's picture
ATAVISMS & VESTIGIAL

ATAVISMS & VESTIGIAL STRUCTURES - COMPELLING EVIDENCE OF MACROEVOLUTION

Our macroevolution deniers have given the fossil record a wide berth, refusing to touch it with a 10-foot pole! So much for that debate. Let's move on to vestigial structures and atavisms, two strong lines of evidence that also scream "macroevolution." Both vestigial structures and atavisms entail an evolutionary past.

A vestigial structure is a structure in a plant or animal that has lost most or all of its original function in the course of evolution. The rudimentary structure is still present in the great majority of individuals and, in some cases, may even have been modified by evolution to perform a useful service! ("Vestigial" doesn't mean "useless.") Here's an example of a vestigial structure: Some species of cave fish have non-functional eyes which are degenerate and covered with skin. They no longer perform their original function but are still hanging around as vestigial structures.

"There is even a blind cave crayfish that still has eyestalks, but no eyes atop them!" (Jerry A. Coyne, "Why Evolution is True", p.60.)

The evolutionary explanation is very simple. No magic mumble jumble. Eyes are useless in the pitch-black darkness of deep caves. Thus, those fish that inherit a bad combination of genes (for their eyes), or a mutated eye gene that doesn't work anymore, are not at risk. Evolution doesn't eliminate fish with poor vision in an environment where vision is useless. So, the evolutionary defects randomly pile up generation after generation until that fish eye no longer works even in daylight. How far this degeneration goes probably depends on how long that species has been living in its dark environment. Some cave fish have no eyes at all!

"To paraphrase the quote from the geneticist Theodosius Dobzhansky that begins this chapter, vestigial traits make sense only in the light of evolution. Sometimes useful, but often not, they're exactly what we'd expect to find if natural selection gradually eliminated useless features or refashioned them into new, more adaptive ones. Tiny, nonfunctional wings, a dangerous appendix, eyes that can't see, and silly ear muscles simply don't make sense if you think that species were specially created." (Jerry A. Coyne, "Why Evolution is True.")

Dr. Coyne has been a professor at the University of Chicago in the Department of Ecology and Evolution for the past 20 years (the cover bio was written in 2009) where he specializes in evolutionary genetics and the origin of new species.

An atavism is a structure in a plant or animal that is normally not present, a kind of throwback in evolutionary time. Atavisms appear in plants and animals from time to time. Example: Some whales occasionally develop the rudimentary structure of hind legs which protrude from their sides. Paleontologists now have the fossils whereby whales can be traced back to four-legged river animals, the ultimate source of this atavism.

The evolutionary explanation is very simple. An evolutionary change that eliminates some structure in an animal (or plant) does not necessarily eliminate the genes for it. A mutation (for example) often disable the mechanism that expresses that gene, leaving the gene intact within the DNA. Generations later, in a few individuals, an unusual combination of genes or new mutations may provide the means to reactivate those ancestral genes. Atavisms only show up now and then because evolution "got rid of" the old structure for a good reason, and its reappearance would require an unusual combination of enabling factors. Nor would it be selected for by evolution unless it fit into a new role. Discontinued genes might still "live" in the DNA, but they are subject to random mutations that would no longer be removed by natural selection. Over geologic time those genes would tend to become degenerate with respect to their original role.

A good example of the above was provided by chickens. As you know, chickens and modern birds don't have teeth. Scarcer than hen's teeth went the old saying. However, the fossil record shows that early birds often had sharp teeth. To make a long story short, scientists were able to supply the means (in a laboratory experiment) to activate those ancient chicken genes for teeth! The experiment was done by E. J. Kollar and C. Fisher in 1980 at the University of Connecticut. The teeth were rudimentary because the genes had, no doubt, collected damaging mutations over the ages. But they were still teeth!

An evolutionary explanation of vestigial structures and atavisms is so natural that it's kind of like falling off of a floating log. I can't hardly wait to see how macroevolution deniers will explain these features! Of course, judging by how fast they ran away from the fossil record, we probably shouldn't expect too much. Do expect total, time-consuming fixations on irrelevant or insignificant details at every turn. Do expect multiple jumps into other topics. Do expect long-established conclusions (used as supporting evidence for macroevolution) to be questioned over and over as though they were debatable. That's my prediction. Place your bets ladies and gentlemen!

Below, are some concrete examples to focus on, taken from "biologydictionary.net, Wikipedia, and Dr. Jerry A. Coyne ("Why Evolution is True"). An excellent book that also hits these subjects along with a solid survey of the fossil record is Dr. Donald Prothero's "Evolution: What the Fossils Say and Why It Matters."

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1) Studies of fruit flies, when various genes were knocked out, produced a wide variety of vestigial structures. In this case the time interval was really, really short! But it does show that vestigial structures can arise naturally from mutated genes.

2) Boas and pythons have vestigial pelvis remnants that protrude as two, small pelvic spurs! "These spurs are sometimes used in copulation, but are not essential, as no colubroid snake (the vast majority of species) possesses these remnants." (Wikipedia - vestigiality). Snakes and other limbless vertebrates occasionally express atavisms in the form of rudimentary hind legs. We also find that snakes have one good lung while the other is shrunken or missing. We thus have a vestigial glimpse of a time when a lizard-like, snake ancestor had two good lungs and four legs.

3) Many whales carry vestigial remnants of hind legs, expressed as a collection of bones that, although detached from the main skeleton, are placed where hind limbs would be expected. In rare cases, for some species of whales, an atavism is expressed whereby degenerate hind legs protrude where legs would have been expected in a land mammal.

…but about one whale in five hundred [of those species that retain vestigial pelvises] is actually born with a rear leg that protrudes outside the body wall. These limbs show all degrees of refinement, with many of them clearly containing the major leg bones of terrestrial mammals--the femur, tibia, and fibula. Some even have feet and toes! (Coyne, p.64)

As Coyne noted, some of that DNA for making legs is still there, though degraded, and there is only one place it could have come from! Any ideas? Fossil discoveries in modern times have now connected the whales to a four-legged river animal, something like a hippo.

4) A classic example of a human vestigial structure is the tailbone or coccyx, a compressed, fused collection of vertebrate. Why would vertebrate, useful for a flexible spine, be squeezed together and fused? Doesn't that speak of a past where something flexible was attached? Our primate ancestors once lived in trees where a long, prehensile tail would have been extremely useful. Working tails are great for trees but not so hot for apes on the ground. It's not surprising that Gorillas, Chimpanzees, and other great apes have lost that tail. Since we trace our evolution through the apes, we don't have a tail either.

A human atavism is sometimes expressed whereby a rudimentary tail comes with the baby! Obviously, we still retain tail-making genes even though they have been degraded by mutations over millions of years.

And they aren't just simple flaps of skin, but can have hair, muscles, blood vessels, and nerves. Some can even wiggle! … What could this mean, other than that we still carry a developmental program for making tails? Indeed, recent genetic work has shown that we carry exactly the same genes that make tails in animals like mice, but these genes are normally deactivated in human fetuses. (Coyne, p.66)

So, we don't get a nice monkey tail! Hmmm, that would make sitting in a nice, stuffed chair a bit awkward!

5) Another classic example of a human vestigial structure is manifested when it gets cold and we get "goosebumps." Small, vestigial muscles at the base of our hair follicles still pull the hairs upright when we get cold, bunching up in contractions (making the goosebumps) as they do so. In our furry ancestors that would make for a fluffier and thicker fur coat that trapped more insulating air, a perfect response to cold weather. Birds fluff their feathers in cold weather for the same reason--to keep warm.

An additional explanation is that many animals, when threatened, puff up their hair to make them look bigger and more formidable. In both cases a fur coat is involved.

6) Flightless birds, such as ostriches and emus, obviously have vestigial wings. Various anatomical structures are present that would make no sense if flight were not in the cards at one time. In the case of the ostrich, its vestigial wings help the bird keep its balance when running about. Note that a vestigial structure, useless for the original purpose, can be adapted to serve other needs. Either way it is compelling evidence for macroevolution.

The vestigial wings of the kiwi, a flightless bird of New Zealand, are so small that they are buried in the feathers of the bird. That it is a vestigial relic of no particular use is the best conclusion anyone can come up with.

7) There are muscles connected to human ears. Most of us can't move our ears diddly-squat, showing that those muscles are not needed. However, you don't have to look very far to see that they are useful for many mammals who point their ears at a suspicious sound for better hearing. Flapping ears also scares away some of the dangerous flies. In those human ear muscles we have a slam-dunk case for a vestigial structure. It takes us way back in time to mammals of a very different type.

8) We humans also have vestigial molecular structures! Example: A gene involved in the making of vitamin C in most other mammals is a useless vestigial structure in us! Think how nice it would be if your body made all the vitamin C that you needed! "A documented mutation deactivated the gene in an ancestor of the modern infraorder of monkeys and apes, and it now remains in their genomes, including the human genome, as a vestigial sequence called a pseudogene." (https://en.wikipedia.org/wiki/vestigiality \cite_note-33)

And the evolutionary prediction that we will find pseudogenes has been fulfilled--amply. Virtually every species harbors dead genes, many of them still active in its relatives. This implies that those genes were also active in a common ancestor, and were killed off in some descendants but not in others. (Coyne, p.67)

Coyne notes that we humans carry more than 2000 pseudogenes, each one pointing back to animals and times when the gene was useful.

9) Except for a few egg-laying mammals, all mammals bear their young live. Thus, they have no need for egg laying. But these mammals still "…carry three genes that, in reptiles and birds, produce the nutritious protein vitellogenin, which fills the yolk sac. But in virtually all mammals these genes are dead, totally inactivated by mutations." (Coyne, p.71). Now, why would we have dead genes for making egg yokes? Egg yokes are necessary for the development of a growing embryo in the laid egg. Mammalian embryos get their sustenance directly from their mother.

"What's more, mammals like ourselves still produce a yolk sac--but one that is vestigial and yolkless, a large, fluid-filled balloon attached to the fetal gut…" (Coyne, p.71-72)

Odd, don't you think? All that vestigial, egg-laying gear points back to a time when our ancestors were egg-laying animals!

10) Dolphins are another interesting showcase for dead, vestigial genes (pseudogenes). Land animals detect all-important odors in the air through a whole suit of olfactory receptor (OR) genes. (Linda Buck and Richard Axel got a Nobel Prize in 2004 for explaining how the olfactory receptors work.)

Detecting odors underwater is another ball game, so dolphins have a completely different set of genes for doing that job. What is interesting is that dolphins also carry the OR genes of land mammals--except that 80% of them are now inactive! Now, why in the world would an ocean-going animal be packing a whole bunch of inactive genes for smelling airborne odors? Tough one! Hint: Maybe they evolved from land animals as indicated by their anatomical details and their DNA.

Most of the old OR genes no longer worked in the ocean and were eventually deactivated by accumulating mutations. Meanwhile, a new system of genes evolved to do the job. Smelling underwater was still important and evolution would favor such adaptations. Macroevolution gives us a natural, magic-free explanation of this very strange situation! (See Coyne, p.69-70 for some interesting additional details.)

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