Free Republic
Browse · Search
Topics · Post Article

Skip to comments.

Truth is a monkey on pols' backs (Richard Cohen: "Half Of America Rejects Theory Of Evolution."
New York Daily News ^ | April 12, 2005 | Richard Cohen

Posted on 04/12/2005 11:29:22 AM PDT by presidio9

Behold the giant Galapagos tortoise! It weighs 700 pounds, lives God-only-knows how long and a couple of weeks ago when I was on the Galapagos Islands, could not be beholden at all. The tortoise we wanted to see, Lonesome George, so called because he is apparently the last of his subspecies, was in hiding. In a sense, that's appropriate because almost half of America cannot see any of the Galapagos for what they are: the home office of evolution. This is where Charles Darwin got his bright idea. It is odd to amble around the Galapagos and see the handiwork of evolution and yet at the same time bear in mind that many Americans do not accept evolution. It is belittled as a mere "theory," which is a misunderstanding of the scientific term, and even in some places where it is grudgingly accepted, it is supposed to share the curriculum with creationism, as if that - creation according to the Bible - is an alternative theory. It is, of course, just a fancy term for the creation according to Genesis, a matter of religious belief and not scientific theory or fact. Each can have its place, but not in the science curriculum.

The ongoing fight over evolution is an odd and sad one. There is nothing about Darwinian theory that cannot be ascribed to God - Darwin himself referred to "the Creator" in his "The Origin of Species" - and back when I was in college and studying evolution, my teacher began the semester by saying, behold the world of God or behold something else: It is entirely up to you.

Yet, 19 states are considering proposals that would require schools to question evolution, which is nothing less than proposals to inject religion into the curriculum. But why stop there? Why not introduce such skepticism into astronomy and have the sun revolve around the Earth or have the Earth stand still? These are questions that Clarence Darrow put to William Jennings Bryan at the so-called Scopes Monkey Trial in 1925. Amazingly, they still linger.

They do so not just because, as Darwin himself conceded, there are holes in the theory of evolution, but because of an evolving political weakness in which intellectual honesty counts for less and less. Thus, you have political leaders from George Bush on down refusing to say whether they put any stock in evolution or believe, as apparently they think they should, that it is an affront and assault on religion. In 1999, Bush was asked whether he was "a creationist." He responded by not responding: "I believe children ought to be exposed to different theories about how the world started." This proves you can go to Yale and learn nothing - not about evolution, mind you, but about intellectual integrity.

The current and ongoing assault on evolution - some Imax theaters, mostly in the South, will not show a film that makes brief references to evolution - is an assault not merely on science, but on thinking and truth and skepticism. Proponents of creationism demand that you stop thinking and instead accept religious dogma.

"There is a grandeur in this view of life," Darwin wrote about his theory.

Behold it.

TOPICS: Culture/Society; Editorial; Philosophy
KEYWORDS: acanthostega; crevolist; evolution; godsgravesglyphs; ichthyostega; science; theory
Navigation: use the links below to view more comments.
first previous 1-20 ... 61-8081-100101-120121-132 next last
To: narby
. . . creationism does so much damage to conservatism . . .

As if your statement is capable of scientific support. As if conservatism depends upon accolades from the left. How much real damage has creationism done? You don't know if it's done any at all. Screw the sanctimonious, pansy-assed fear.

101 posted on 04/12/2005 8:28:03 PM PDT by Fester Chugabrew
[ Post Reply | Private Reply | To 22 | View Replies]

To: freedomfiter2
Maybe scientists will consider anything but they will not allow the conflicting facts which show that the theory of evolution still has many wrinkles to iron out.

Please document this amazing claim of yours.

It's no accident that most major leaps of science have been made by scientists who were somewhat on the fringes of the science community.

"Most"? Please document *this* amazing claim too while you're at it.

102 posted on 04/12/2005 8:42:29 PM PDT by Ichneumon
[ Post Reply | Private Reply | To 49 | View Replies]

To: wideawake
Genesis does contradict itself in specific sequences of actions.

No it doesn't. Cite one single example.

Order of Creation

Genesis 1

Plants-->Animals--> Man & Woman simultaneously

Genesis 2

Man -->Plants-> Animals--> Woman

Did the fowls come from the waters

1:20 And God said, Let the waters bring forth abundantly the moving creature that hath life, and fowl that may fly above the earth in the open firmament of heaven.

1:21 And God created great whales, and every living creature that moveth, which the waters brought forth abundantly, after their kind, and every winged fowl after his kind: and God saw that it was good.

Or  ground?

2:19 And out of the ground the LORD God formed every beast of the field, and every fowl of the air; and brought them unto Adam to see what he would call them: and whatsoever Adam called every living creature, that was the name thereof.

103 posted on 04/12/2005 9:00:30 PM PDT by qam1 (There's been a huge party. All plates and the bottles are empty, all that's left is the bill to pay)
[ Post Reply | Private Reply | To 78 | View Replies]

To: E-Mat; PatrickHenry; 3dognight; <1/1,000,000th%; Agamemnon; ClearCase_guy; Fester Chugabrew; ...
What evidence of evolution is as strong as the evidence I just mentioned?

Well, here are some recent FreeRepublic posts of mine which describe some of the evidence of evolution (and despite the size of them, this is just the *tip* of the iceberg -- I could choke the server if I posted a substantial fraction of it):

Human/ape common ancestry:

This is just a taste of the massive amount of evidence for ape/human common ancestry, the amount for evolution in general (including between different specific animal families) would (and does) fill innumerable encyclopedias worth of volumes:

Background: Retroviruses reproduce by entering a cell of a host (like, say, a human), then embedding their own viral DNA into the cell's own DNA, which has the effect of adding a "recipe" for manufacturing more viruses to the cell's "instruction book". The cell then follows those instructions because it has no reason (or way) to "mistrust" the DNA instructions it contains. So the virus has converted the cell into a virus factory, and the new viruses leave the cell, and go find more cells to infect, etc.

Image Hosted by

However, every once in a while a virus's invasion plans don't function exactly as they should, and the virus's DNA (or portions of it) gets embedded into the cell's DNA in a "broken" manner. It's stuck into there, becoming part of the cell's DNA, but it's unable to produce new viruses. So there it remains, causing no harm. If this happens in a regular body cell, it just remains there for life as a "fossil" of the past infection and goes to the grave with the individual it's stuck in. All of us almost certainly contain countless such relics of the past viral infections we've fought off.

However... By chance this sometimes happens to a special cell in the body, a gametocyte cell that's one of the ones responsible for making sperm in males and egg cells in females, and if so subsequent sperm/eggs produced by that cell will contain copies of the "fossil" virus, since now it's just a portion of the entire DNA package of the cell. And once in a blue moon such a sperm or egg is lucky enough to be one of the few which participate in fertilization and are used to produce a child -- who will now inherit copies of the "fossilized" viral DNA in every cell of his/her body, since all are copied from the DNA of the original modified sperm/egg.

So now the "fossilized" viral DNA sequence will be passed on to *their* children, and their children's children, and so on. Through a process called neutral genetic drift, given enough time (it happens faster in smaller populations than large) the "fossil" viral DNA will either be flushed out of the population eventually, *or* by luck of the draw end up in every member of the population X generations down the road. It all depends on a roll of the genetic dice.

Due to the hurdles, "fossil" retroviral DNA strings (known by the technical name of "endogenous retroviruses") don't end up ubiquitous in a species very often, but it provably *does* happen. In fact, the Human DNA project has identified literally *thousands* of such fossilized "relics" of long-ago ancestral infections in the human DNA.

And several features of these DNA relics can be used to demonstrate common descent, including their *location*. The reason is that retroviruses aren't picky about where their DNA gets inserted into the host DNA. Even in an infection in a *single* individual, each infected cell has the retroviral DNA inserted into different locations than any other cell. Because the host DNA is so enormous (billions of basepairs in humans, for example), the odds of any retroviral insertion event matching the insertion location of any other insertion event are astronomically low. The only plausible mechanism by which two individuals could have retroviral DNA inserted into exactly the same location in their respective DNAs is if they inherited copies of that DNA from the same source -- a common ancestor.

Thus, shared endogenous retroviruses between, say, ape and man is almost irrefutable evidence that they descended from a common ancestor. *Unless* you want to suggest that they were created separately, and then a virus they were both susceptible to infected both a man and an ape in EXACTLY the same location in their DNAs (the odds of such a match by luck are literally on the order of 1,000,000,000,000,000,000 to 1...), *and* that the infections both happened in their gametocyte cells (combined odds on the order of 1,000,000 to 1) *and* that the one particular affected gametocyte is the one which produces the egg or sperm which is destined to produce an offspring (*HUGE* odds against), and *then* the resulting modified genome of the offspring becomes "fixed" in each respective population (1 out of population_size^squared)...

Then repeat that for *each* shared endogenous retrovirus (there are many) you'd like to claim was acquired independently and *not* from a shared ancestor...

Finally, you'd have to explain why, for say species A, B, and C, the pattern of shared same-location retroviruses is always *nested*, never *overlapped*. For example, all three will share some retroviruses, then A and B will both share several more, but if so then B *never* shares one with C that A doesn't also have (or at least remnants of).

In your "shared infection due to genetic similarities" suggestion, even leaving aside the near statistical impossibility of the infections leaving genetic "scars" in *exactly* the same locations in independent infections, one would expect to find cases of three species X, Y, and Z, where the degree of similarity was such that Y was "between" X and Z on some similarity scale, causing the same disease to befall X and Y but not Z, and another disease to affect Y and Z but not X. And yet, we don't find this in genetic markers. The markers are found in nested sequence, which is precisely what we would expect to see in cases of inheritance from common ancestry.

Here, for example, is an ancestry tree showing the pattern of shared same-location endogenous retroviruses of type HERV-K among primates:

This is just a partial list for illustration purposes -- there are many more.

Each labeled arrow on the chart shows an ERV shared in common by all the branches to the right, and *not* the branches that are "left-and-down". This is the pattern that common descent would make. And common descent is the *only* plausible explanation for it. Furthermore, similar findings tie together larger mammal groups into successively larger "superfamilies" of creatures all descended from a common ancestor.

Any presumption of independent acquisition is literally astronomically unlikely. And "God chose to put broken relics of viral infections that never actually happened into our DNA and line them up only in patterns that would provide incredibly strong evidence of common descent which hadn't actually happened" just strains credulity (not to mention would raise troubling questions about God's motives for such a misleading act).

Once again, the evidence for common descent -- as opposed to any other conceivable alternative explanation -- is clear and overwhelming.

Wait, want more? Endogenous retroviruses are just *one* type of genetic "tag" that makes perfect sense evolutionary and *no* sense under any other scenario. In addition to ERV's, there are also similar arguments for the patterns across species of Protein functional redundancies, DNA coding redundancies, shared Processed pseudogenes, shared Transposons (including *several* independent varieties, such as SINEs and LINEs), shared redundant pseudogenes, etc. etc. Here, for example, is a small map of shared SINE events among various mammal groups:

Like ERV's, any scenario which suggests that these shared DNA features were acquired separately strains the laws of probability beyond the breaking point, but they make perfect sense from an evolutionary common-descent scenario. In the above data, it is clear that the only logical conclusion is that, for example, the cetaceans, hippos, and ruminants shared a common ancestor, in which SINE events B and C entered its DNA and then was passed on to its descendants, yet this occurred after the point in time where an earlier common ancestor had given rise both to that species, and to the lineage which later became pigs.

And this pattern (giving the *same* results) is repeated over and over and over again when various kinds of molecular evidence from DNA is examined in detail.

The molecular evidence for evolution and common descent is overwhelming. The only alternative is for creationists to deny the obvious and say, "well maybe God decided to set up all DNA in *only* ways that were consistent with an evolutionary result even though He'd have a lot more options open to him, even including parts which by every measure are useless and exactly mimic copy errors, ancient infections, stutters, and other garbage inherited from nonexistent shared ancestors"...

Or how about:
Humans have 23 pairs of chromosomes ---chimps and gorillas have 24 pairs. How many pairs of chromosomes did the "common ancestor" have? Was it 23 or 24 pairs? How do you "evolve" missing or added chromosomes ---that would happen all at one time.

The common ancestor had 24 chromosomes.

If you look at the gene sequences, you'll find that Chromosome 2 in humans is pretty much just 2 shorter chimpanzee chromosomes pasted end-to-end, with perhaps a slight bit of lost overlap:

(H=Human, C=Chimpanzee, G=Gorilla, O=Orangutan)

Somewhere along the line, after humans split off from the other great apes, or during the split itself, there was an accidental fusion of two chromosomes, end-to-end. Where there used to be 24 chromosomes, now there were 23, but containing the same total genes, so other than a "repackaging", the DNA "instructions" remained the same.

If a chimpanzee gives birth to a creature with 23 chromosomes, that offspring isn't going to be a well-formed chimpanzee able to survive well.

It is if the same genes are present, which they would be in the case of a chromosome fusion.

Evolve would imply the genetic material changes little by little --not some big loss of two chromosomes at once but I don't see how they'd go away gene by gene.

Tacking two chromosomes together end-to-end is not a "big loss" of genes, and it really is a "little by little" change in the total genetic code. It's just been "regrouped" a bit. Instead of coming in 24 "packages", it's now contained in 23, but the contents are the same.

So how, you might ask, would the chromosomes from the first 23-chromosome "fused" individual match up with the 24 chromosomes from its mate when it tried to produce offspring? Very well, thanks for asking. The "top half" of the new extra-long Chromosome 2 would adhere to the original chromosome (call it "2p") from which it was formed, and likewise for the "bottom half" which would adhere to the other original shorter chromosome (call it "2q"). In the picture above, imagine the two chimp chromosomes sliding over to "match up" against the human chromosome. The chimp chromosomes would end up butting ends with each other, or slightly overlapping in a "kink", but chromosomes have overcome worse mismatches (just consider the XY pair in every human male -- the X and the Y chromosome are *very* different in shape, length, and structure, but they still pair up).

In fact, the "rubbing ends" of the matched-up chimp chromosomes, adhering to the double-long human-type chromosome, would be more likely to become fused together themselves.

For studies in which recent chromosome fusions have been discovered and found not to cause infertility, see:

Chromosomal heterozygosity and fertility in house mice (Mus musculus domesticus) from Northern Italy. Hauffe HC, Searle JB Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.

An observed chromosome fusion: Hereditas 1998;129(2):177-80 A new centric fusion translocation in cattle: rob (13;19). Molteni L, De Giovanni-Macchi A, Succi G, Cremonesi F, Stacchezzini S, Di Meo GP, Iannuzzi L Institute of Animal Husbandry, Faculty of Agricultural Science, Milan, Italy.

J Reprod Fertil 1979 Nov;57(2):363-75 Cytogenetics and reproduction of sheep with multiple centric fusions (Robertsonian translocations). Bruere AN, Ellis PM

J Reprod Fertil Suppl 1975 Oct;(23):356-70 Cytogenetic studies of three equine hybrids. Chandley AC, Short RV, Allen WR.

In that last reference, the Przewalski horse, which has 33 chromosomes, and the domestic horse, with 32 chromosomes (due to a fusion), are able to mate and produce fertile offspring.

Meanwhile, the question may be asked, how do we know that the human Chromosome 2 is actually the result of a chromsome fusion at/since a common ancestor, and not simply a matter of "different design"?

Well, if two chromsomes accidentally merged, there should be molecular remnants of the original chromosomal structures (while a chromosome designed from scratch would have no need for such leftover "train-wreck" pieces).

Ends of chromosomes have characteristic DNA base-pair sequences called "telomeres". And there are indeed remnants of telomeres at the point of presumed fusion on human Chromosome 2 (i.e., where the two ancestral ape chromosomes merged end-to-end). If I may crib from a web page:

Telomeres in humans have been shown to consist of head to tail repeats of the bases 5'TTAGGG running toward the end of the chromosome. Furthermore, there is a characteristic pattern of the base pairs in what is called the pre-telomeric region, the region just before the telomere. When the vicinity of chromosome 2 where the fusion is expected to occur (based on comparison to chimp chromosomes 2p and 2q) is examined, we see first sequences that are characteristic of the pre-telomeric region, then a section of telomeric sequences, and then another section of pre-telomeric sequences. Furthermore, in the telomeric section, it is observed that there is a point where instead of being arranged head to tail, the telomeric repeats suddenly reverse direction - becoming (CCCTAA)3' instead of 5'(TTAGGG), and the second pre-telomeric section is also the reverse of the first telomeric section. This pattern is precisely as predicted by a telomere to telomere fusion of the chimpanzee (ancestor) 2p and 2q chromosomes, and in precisely the expected location. Note that the CCCTAA sequence is the reversed complement of TTAGGG (C pairs with G, and T pairs with A).
Another piece of evidence is that if human Chromosome 2 had formed by chromosome fusion in an ancestor instead of being designed "as is", it should have evidence of 2 centromeres (the "pinched waist" in the picture above -- chromosomes have centromeres to aid in cell division). A "designed" chromosome would need only 1 centromere. An accidentally "merged" chromosome would show evidence of the 2 centromeres from the two chromosomes it merged from (one from each). And indeed, as documented in (Avarello R, Pedicini A, Caiulo A, Zuffardi O, Fraccaro M, Evidence for an ancestral alphoid domain on the long arm of human chromosome 2. Hum Genet 1992 May;89(2):247-9), the functional centromere found on human Chromosome 2 lines up with the centromere of the chimp 2p chromosome, while there are non-functional remnants of the chimp 2q centromere at the expected location on the human chromosome.

As an aside, the next time some creationist claims that there is "no evidence" for common ancestry or evolution, keep in mind that the sort of detailed "detective story" discussed above is repeated literally COUNTLESS times in the ordinary pursuit of scientific research and examination of biological and other types of evidence. Common ancestry and evolution is confirmed in bit and little ways over and over and over again. It's not just something that a couple of whacky anti-religionists dream up out of thin air and promulgate for no reason, as the creationists would have you believe.

[The poster known as Mr. LLLICHY wrote:] Here is that Vitamin C data

After discovering this same data on another thread along with more discussion than has appeared here (I've taken the liberty of pinging the participants of that discussion), I see what the "mystery" is supposed to be -- it's supposed be why did some sites have multiple mutations while (small) stretches of other sites had none? In other words, why do the mutations appear clustered?

(You know, it would really help if people explained their points and questions in more detail, instead of leaving people to guess what the poster was thinking...)

[LLLICHY wrote:] "U238" that decays thrice, pretty good trick when there is "U238" that does not decay at all in 50,000,000 years.

Actually, no site had mutations "thrice". Three different bases at a given site is only *two* mutations (one original base, plus two mutations from it to something else).

Here's the "mutation map" from the actual DNA data:

--1-12--1-1-1-1--------1112112--1---1-11-1--------1 ALL/n
No mutations ("-") in about half the sites, one mutation at several (17) sites, two mutations at three sites.

The first thing to keep in mind that random processes tend to "cluster" more than people expect anyway. People expect "randomness" to "spread out" somewhat evenly, but instead it's usually more "clumped", for statistical reasons that would be a diversion to go into right now. So "that looks uneven" isn't always a good indication that something truly is non-random.

If you don't believe me on that, I wrote a program which made 23 mutations totally at random on a 51-site sequence, then repeated the process to see what different random outcomes would look like:

10 X$=STRING$(51,"-")
20 FOR I=1 TO 23
30 J%=INT(RND*51)+1
40 C$=MID$(X$,J%,1)
50 IF C$="-" THEN MID$(X$,J%,1)="1" ELSE MID$(X$,J%,1)=CHR$(ASC(C$)+1)
80 GOTO 10
Yeah, it's BASIC, so sue me. Here's a typical screenful of the results:
Notice how oddly "clustered" most of them look, including one run which left a 13-site stretch "absolutely untouched", contrary to intuition (while having *4* mutations at a single site!)

Frankly, I don't see anything in the real-life DNA mutation map which looks any different from these truly random runs. Random events tend to cluster more than people expect. That solves the "mystery" right there.

Also, there may be a selection factor -- the GLO gene is a *lot* bigger than this. One has to wonder if this small 51-bp section was presented just because it was the one that looked "least random". That would be a no-no, since one can always hand-select the most deviant subset out of larger sample in order to artificially skew the picture.

However, since there are some interesting evolutionary observations to be made, let's look at that DNA data again, slightly rearranged:




Here I've put spaces between codons, and clustered the closely-related species together: pig/cow as ungulates, rat/mouse for their obvious relationship, guinea pig right below them but separated because of the pseudogene nature of its GLO gene, then primates all in a group, with man's closest relative, the chimp, immediately below him, followed by the more distant orangutan, and the even more distant macaque. Also note that the top four have "working" GLO genes, and the bottom five have "broken" GLO pseudogenes.

First, let's consider just the four species with working GLO genes. Evolution predicts that even over large periods of time, these genes will be "highly conserved", with natural selection weeding out mutations that could "break" the gene. Note that the mutations will still have occurred in individuals of the population, but natural selection will "discourage" that mutation from spreading into the general population.

And before we go any further, let's talk about the "universal genetic code". In all mammals (indeed, in almost all living organisms), each triplet of DNA sites cause a particular amino acid to be formed. The mapping of triplets (called "codons") to amino acids is as follows:

Second Position of Codon

TTT Phe [F]
TTC Phe [F]
TTA Leu [L]
TTG Leu [L]
TCT Ser [S]
TCC Ser [S]
TCA Ser [S]
TCG Ser [S]
TAT Tyr [Y]
TAC Tyr [Y]
TAA Ter [end]
TAG Ter [end]
TGT Cys [C]
TGC Cys [C]
TGA Ter [end]
TGG Trp [W]

CTT Leu [L]
CTC Leu [L]
CTA Leu [L]
CTG Leu [L]
CCT Pro [P]
CCC Pro [P]
CCA Pro [P]
CCG Pro [P]
CAT His [H]
CAC His [H]
CAA Gln [Q]
CAG Gln [Q]
CGT Arg [R]
CGC Arg [R]
CGA Arg [R]
CGG Arg [R]
ATT Ile [I]
ATC Ile [I]
ATA Ile [I]
ATG Met [M]
ACT Thr [T]
ACC Thr [T]
ACA Thr [T]
ACG Thr [T]
AAT Asn [N]
AAC Asn [N]
AAA Lys [K]
AAG Lys [K]
AGT Ser [S]
AGC Ser [S]
AGA Arg [R]
AGG Arg [R]
GTT Val [V]
GTC Val [V]
GTA Val [V]
GTG Val [V]
GCT Ala [A]
GCC Ala [A]
GCA Ala [A]
GCG Ala [A]
GAT Asp [D]
GAC Asp [D]
GAA Glu [E]
GAG Glu [E]
GGT Gly [G]
GGC Gly [G]
GGA Gly [G]
GGG Gly [G]

(The above table imported from, which also has a nice introduction to the genetic code.)

Another version of the same table with nifty Java features and DNA database lookups can be found here.

The thing which is most relevant to the following discussion is the fact that most of the genetic codes are "redundant" -- more than one codon (triplet) encodes to exactly the same amino acid. This means that even in genes which are required for the organism, certain basepair mutations make absolutely no difference if the change is from one codon which maps into amino acid X to another codon which still maps into amino acid X. (This fact allows certain kinds of evolutionary "tracers" to be "read" from the DNA, as described here).

Now back to our DNA data. The redundancy in the genetic code means that some basepair sites will have more "degrees of freedom" than others (i.e., ways in which they can mutate without disrupting the gene's biological function in any way). Let's look at the four species with working GLO genes again:

  T   T   T   A   T A T   T   T A T   C   C   T   T T T T T   T   T
      A   A       A   A       A   C   A           A   A   A       A
      G   C       G   G       G   G   G               C   C       C
--- --- --1 --- --1 --- --- --1 --2 -12 --1 --- --1 --- --- --- --1

Under each site of the mouse DNA, I've listed the "alternative" bases which could be be substituted for the mouse base at that site WITHOUT ALTERING THE GENE'S FUNCTION (because of genetic code redundancy). And under that I show the "mutation map" of just those four species.

Note that most of the "alternative" bases are in the third base of each codon, *and* that this is where all but one of the mutations have appeared. This is because these were the sites which were "free" to mutate in the way they did, because the mutation was genetically neutral. That doesn't mean that the first and second sites of each codon were immune from mutation, it's just that when mutations did occur at those sites, natural selection weeded them out quickly because they most likely "broke" the GLO gene for the individuals which received that mutuation. What we see above is the results after natural selection has already "filtered" the undesirable mutations and left the ones which "do no harm".

Additionally, the two sites which have mutated twice (i.e. have a "2" in the mutation map) are ones which had more "allowable" mutations. Also note that the sites which had the fewest allowable alternatives (only one alternate letter allowed) didn't have any mutations fix at those sites, which is unsurprising since a "safe" mutation would be less likely to occur there versus a site that "allowed" two or three alternatives.

All this is as predicted by evolutionary theory, you'll note.

It also explains the one anomoly of the original mutation map, which is that the mutation counts do tend to be higher at the third base of a codon.

However... What about the one exception? The pig DNA has had one mutation at a site which does not encode to exactly the same amino acid (which is the case for *all* the other ones). In the pig DNA, the GGG codon (mapping to Glycine) has changed to a GCG codon (mapping to Alanine). What's up with that? Well, one of two things. First and most likely, just as base values in codons have a built-in redundancy, so do the amino acids which make up the proteins which result from the DNA templates. In other words, certain amino acids can be substituted for other ones at some sites in given proteins without making any functional difference. (This "protein functional redundancy" also has implications for "evolutionary tracer" analysis, see here.) That may well be the case for Alanine versus Glycine in the GLO protein, but I'm not enough of a biochemist to be able to say. The other option is that it *does* make some difference in the function of the pig GLO protein, but not enough to "break" the vitamin-C synthesis (as proven by the fact that pigs *can* synthesize vitamin C). So one way or another, it's not a deal-breaker even though pig GLO will not be 100% identical to cow/mouse/rat GLO. It's yet another "allowable" mutation.

More interesting evolutionary observations: The number of mutational differences between pig/cow is 3, the number between mouse/rat is 4, and the difference between rat/cow is 7 -- all roughly as one would expect from the evolutionary relatedness of these animals (cows/pigs and rats/mice are each closer to each other than the rodents are to the ungulates).

Now let's take a close look at the guinea pig:

--- --1 --- -1- --- --- --- --- --1 --1 --1 --- --- --- --- --- ---
The "mutation map" under the guinea pig DNA is compared to the mouse DNA. Fascinating: Note that four of the five mutations are in the third base of a codon, *and* are of the type "allowed" by the genetic code redundancy. This indicates strongly that most of the evolutionary divergence between guinea pigs and mice likely occurred while the guinea pig's ancestors still had a working GLO gene. This is the sort of prediction implied by the evolutionary theory which could be cross-checked by further research of various types, and if verified, would be yet further confirmation that evolutionary theory is likely correct. So far, evolutionary theory has been subjected to literally countless tests like this, large and small, and the vast majority of results have confirmed the evolutionary prediction. This track record is hard to explain if evolution is an invalid theory, as some assert...

Finally, let's look over the primate DNA and mutation map (relative to each other):

--1 -1- --- --- 1-1 --- --- --- 111 1-- --- --- 1-- 1-- --- --- ---
Evolutionary theory predicts that because the GLO gene is "broken" in primates (i.e. is a pseudogene), mutations in it are highly likely to be neutral (i.e., make no difference, since it can't get much more broken), and thus mutations are just as likely to accumulate at any site as any other. Is that what we see? Yup. There's no obvious pattern to the mutations between primates in the above mutation map, and unlike the pig/cow/mouse/rat mutation map, the mutations aren't predominantly at the "safer" third base of a codon, nor of a type that would be "safe". In fact, one base has vanished entirely, but no biggie, the gene's already broken.

Also, although primates share a more recent common ancestor than cows/pigs/mice/rats, note that they've already racked up almost as many relative mutations as the cow/pig/mouse/rat DNA. This too is just as evolutionary theory predicts, because many mutations in a functional gene (GLO in this case) will be "non-safe" and weeded out by natural selection, making for a slower mutation fixation rate overall than in a pseudogene (as GLO is in primates) where natural selection doesn't "care" about the vast majority of mutations since *most* are neutral. So pseudogenes accumulate mutations faster than functional genes (even though rate of mutation *occurence* in both are likely the same).

Finally, note that there are ZERO mutational differences between the human DNA and the chimpanzee DNA, our nearest living relative.

I also see some interesting implications in the DNA sequences concerning which specific mutation fixed during what branch of the common-descent evolutionary tree for all the species represented, but reconstructing that would not only take another couple hours, at least, but would be a major bear to code in HTML, since I'd have to draw trees with annotations on the nodes... Bleugh.

In any case, I hope I've clarified some of the methods by which biologists find countless confirmations of evolution in DNA data. This is just a "baby" example, and to be more statistically valid would have to be done over much vaster sections of DNA sequences, but my intent was to demonstrate some of the concepts.

And if such a small amount of DNA as this can make small confirmations of evolutionary predictions, imagine the amount of confirmation from billion-basepair DNA data from each species compared across thousands of species... The amount of confirmatory discoveries for evolution from DNA analysis has already been vast, and promises to only grow in the future. For an overview of some of the different lines of evidence being studied, see The Journal of Molecular Evolution -- abstracts of all articles, current and back issues, can be browsed free online.

See also, for example (out of thousands):
Analysis of the human Alu Ye lineage

Human endogenous retrovirus HERV-K14 families: status, variants, evolution, and mobilization of other cellular sequences

Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences

Molecular and temporal characteristics of human retropseudogenes.

Evolution of RPS4Y

Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution

Serine hydroxymethyltransferase pseudogene, SHMT-ps1: a unique genetic marker of the order primates

Structure and phylogenetic analysis of an endogenous retrovirus inserted into the human growth factor gene pleiotrophin

Molecular evolution of cytochrome c oxidase subunit IV: evidence for positive selection in simian primates

The ZNF75 zinc finger gene subfamily: isolation and mapping of the four members in humans and great apes

Insertions and duplications of mtDNA in the nuclear genomes of Old World monkeys and hominoids

Conservation of sequences between human and gorilla lineages: ADP-ribosyltransferase (NAD+) pseudogene 1 and neighboring retroposons

Fixation times of retroposons in the ribosomal DNA spacer of human and other primates

The gamma-globin genes and their flanking sequences in primates: findings with nucleotide sequences of capuchin monkey and tarsier

The emergence of new DNA repeats and the divergence of primates

Genetic diversity at class II DRB loci of the primate MHC

Nucleotide sequences of immunoglobulin-epsilon pseudogenes in man and apes and their phylogenetic relationships

Structure and evolution of human and African ape rDNA pseudogenes

How many more would you like?

Reptile -> Mammal evolutionary transition:

Example 2: reptile-mammals

[Figure1.4.1 (cartoon of vertebrate jaws)]

Figure 1.4.1. The jaws of three vertebrates—mammal, therapsid, and pelycosaur. A side view of three idealized skulls of mammals, therapsids (mammal-like reptiles), and pelycosaurs (early reptiles). The figure shows the differences between mammal and reptilian jaws and ear-bone structures. The jaw joint is shown as a large black dot, the quadrate (mammalian anvil or incus) is in turquoise, the articular (mammalian hammer or malleus) is in yellow, and the angular (mammalian tympanic annulus) is in pink. Note how, in the reptile, the jaw joint is formed between the blue quadrate and the yellow articular (with the pink angular close by), and how, in the mammal, the jaw joint is formed between the squamosal above and the dentary below. In the reptile, the squamosal is just above and contacting the quadrate. Advanced therapsids have two jaw joints: a reptile-like joint and a mammal-like joint (Figure based on Kardong 2002, pp. 275, reproduced with permission from the publisher, Copyright © 2002 McGraw-Hill)

We also have an exquisitely complete series of fossils for the reptile-mammal intermediates, ranging from the pelycosauria, therapsida, cynodonta, up to primitive mammalia (Carroll 1988, pp. 392-396; Futuyma 1998, pp. 146-151; Gould 1990; Kardong 2002, pp. 255-275). As mentioned above, the standard phylogenetic tree indicates that mammals gradually evolved from a reptile-like ancestor, and that transitional species must have existed which were morphologically intermediate between reptiles and mammals—even though none are found living today. However, there are significant morphological differences between modern reptiles and modern mammals. Bones, of course, are what fossilize most readily, and that is where we look for transitional species from the past. Osteologically, two major striking differences exist between reptiles and mammals: (1) reptiles have at least four bones in the lower jaw (e.g. the dentary, articular, angular, surangular, and coronoid), while mammals have only one (the dentary), and (2) reptiles have only one middle ear bone (the stapes), while mammals have three (the hammer, anvil, and stapes) (see Figure 1.4.1).

Early in the 20th century, developmental biologists discovered something that further complicates the picture. In the reptilian fetus, two developing bones from the head eventually form two bones in the reptilian lower jaw, the quadrate and the articular (see the Pelycosaur in Figure 1.4.1). Surprisingly, the corresponding developing bones in the mammalian fetus eventually form the anvil and hammer of the unique mammalian middle ear (also known more formally as the incus and malleus, respectively; see Figure 1.4.2) (Gilbert 1997, pp. 894-896). These facts strongly indicated that the hammer and anvil had evolved from these reptilian jawbones—that is, if common descent was in fact true. This result was so striking, and the required intermediates so outlandish, that many anatomists had extreme trouble imagining how transitional forms bridging these morphologies could have existed while retaining function. Young-earth creationist Duane Gish stated the problem this way:

"All mammals, living or fossil, have a single bone, the dentary, on each side of the lower jaw, and all mammals, living or fossil, have three auditory ossicles or ear bones, the malleus, incus and stapes. ... Every reptile, living or fossil, however, has at least four bones in the lower jaw and only one auditory ossicle, the stapes. ... There are no transitional fossil forms showing, for instance, three or two jawbones, or two ear bones. No one has explained yet, for that matter, how the transitional form would have managed to chew while his jaw was being unhinged and rearticulated, or how he would hear while dragging two of his jaw bones up into his ear." (Gish 1978, p. 80)

[Figure1.4.2a (cartoon of vertebrate ears)] [Figure1.4.2b (cartoon of vertebrate ears)]

Figure 1.4.2. A comparison of the ears of reptiles and mammals. The reptile ear is shown on the left, the mammal ear on the right. As in Figure 1.4.1, the quadrate (mammalian anvil or incus) is in turquoise and the articular (mammalian hammer or malleus) is in yellow. The stapes is shown in brown. Note how the relative arrangement of these bones is similar in both taxa, in the order of inner ear-stapes-quadrate-articular.

Gish was incorrect in stating that there were no transitional fossil forms, and he has been corrected on this gaff numerous times since he wrote these words. However, Gish's statements nicely delineate the morphological conundrum at hand. Let's review the required evolutionary conclusion. During their evolution, two mammalian middle ear bones (the hammer and anvil, aka malleus and incus) were derived from two reptilian jawbones. Thus there was a major evolutionary transition in which several reptilian jawbones (the quadrate, articular, and angular) were extensively reduced and modified gradually to form the modern mammalian middle ear. At the same time, the dentary bone, a part of the reptilian jaw, was expanded to form the major mammalian lower jawbone. During the course of this change, the bones that form the hinge joint of the jaw changed identity. Importantly, the reptilian jaw joint is formed at the intersection of the quadrate and articular whereas the mammalian jaw joint is formed at the intersection of the squamosal and dentary (see Figure 1.4.1).

How could hearing and jaw articulation be preserved during this transition? As clearly shown from the many transitional fossils that have been found (see Figure 1.4.3), the bones that transfer sound in the reptilian and mammalian ear were in contact with each other throughout the evolution of this transition. In reptiles, the stapes contacts the quadrate, which in turn contacts the articular. In mammals, the stapes contacts the incus, which in turn contacts the malleus (see Figure 1.4.2). Since the quadrate evolved into the incus, and the articular evolved into the malleus, these three bones were in constant contact during this impressive evolutionary change. Furthermore, a functional jaw joint was maintained by redundancy—several of the intermediate fossils have both a reptilian jaw joint (from the quadrate and articular) and a mammalian jaw joint (from the dentary and squamosal). Several late cynodonts and Morganucodon clearly have a double-jointed jaw. In this way, the reptilian-style jaw joint was freed to evolve a new specialized function in the middle ear. It is worthy of note that some modern species of snakes have a double-jointed jaw involving different bones, so such a mechanical arrangement is certainly possible and functional.

Since Figure 1.4.3 was made, several important intermediate fossils have been discovered that fit between Morganucodon and the earliest mammals. These new discoveries include a complete skull of Hadrocodium wui (Luo et al. 2001) and cranial and jaw material from Repenomamus and Gobiconodon (Wang et al. 2001). These new fossil finds clarify exactly when and how the malleus, incus, and angular completely detached from the lower jaw and became solely auditory ear ossicles.

Recall that Gish stated: "There are no transitional fossil forms showing, for instance, three or two jawbones, or two ear bones" (Gish 1978, p. 80). Gish simply does not understand how gradual transitions happen (something he should understand, obviously, if he intends to criticize evolutionary theory). These fossil intermediates illustrate why Gish's statement is a gross mischaracterization of how a transitional form should look. In several of the known intermediates, the bones have overlapping functions, and one bone can be called both an ear bone and a jaw bone; these bones serve two functions. Thus, there is no reason to expect transitional forms with intermediate numbers of jaw bones or ear bones. For example, in Morganucodon, the quadrate (anvil) and the articular (hammer) serve as mammalian-style ear bones and reptilian jaw bones simultaneously. In fact, even in modern reptiles the quadrate and articular serve to transmit sound to the stapes and the inner ear (see Figure 1.4.2). The relevant transition, then, is a process where the ear bones, initially located in the lower jaw, become specialized in function by eventually detaching from the lower jaw and moving closer to the inner ear.

[Figure1.4.3 (cartoon of vertebrate jaws)]

Figure 1.4.3. A comparison of the jawbones and ear-bones of several transitional forms in the evolution of mammals. Approximate stratigraphic ranges of the various taxa are indicated at the far left (more recent on top). The left column of jawbones shows the view of the left jawbone from the inside of the mouth. The right column is the view of the right jawbone from the right side (outside of the skull). As in Figure 1.4.1, the quadrate (mammalian anvil or incus) is in turquoise, the articular (mammalian hammer or malleus) is in yellow, and the angular (mammalian tympanic annulus) is in pink. For clarity, the teeth are not shown, and the squamosal upper jawbone is omitted (it replaces the quadrate in the mammalian jaw joint, and forms part of the jaw joint in advanced cynodonts and Morganucodon). Q = quadrate, Ar = articular, An = angular, I = incus (anvil), Ma = malleus (hammer), Ty = tympanic annulus, D = dentary. (Reproduced from Kardong 2002, pp. 274, with permission from the publisher, Copyright © 2002 McGraw-Hill)

The above is from 29+ Evidences for Macroevolution, which compiles several hundred transitional fossils, which is itself just a *SMALL* sampling of the ENORMOUS numbers of fine transitional sequences found in the fossil record and well known to anyone who has bothered to CRACK OPEN A BOOK -- or even do a websearch -- in the past 25 years or so... So what's the anti-evolutionists' excuse for remaining abysmally ignorant of such things, and repeatedly making the false claim that there are "no" transitional fossils, etc.?

Here's another look:

Mammal-Like Reptiles

As previously stated, a succession of transitional fossils exists that link reptiles (Class Reptilia) and mammals (Class Mammalia). These particular reptiles are classifie as Subclass Synapsida. Presently, this is the best example of th e transformation of one major higher taxon into another. The morphologic changes that took place are well documented by fossils, beginning with animals essentially 100% reptilian and resulting in animals essentially 100% mammalian. Therefore, I have chosen this as the example to summarize in more detail (Table 1, Fig. 1).

[Fig. 1a]
[Fig. 1b]

Skulls and jaws of synapsid reptiles and mammals; left column side view of skull; center column top view of skull; right column side view of lower jaw. Hylonomus modified from Carroll (1964, Figs. 2,6; 1968, Figs. 10-2, 10-5; note that Hylonomus is a protorothyrod, not a synapsid). Archaeothyris modified from Reisz (1972, Fig. 2). Haptodus modified from Currie (1977, Figs, 1a, 1b; 1979, Figs. 5a, 5b). Sphenacodo n modified from Romer & Price (1940, Fig. 4f), Allin (1975, p. 3, Fig. 16);note: Dimetrodon substituted for top view; modified from Romer & Price, 1940, pl. 10. Biarmosuchus modified from Ivakhnenko et al. (1997, pl. 65, Figs. 1a, 1B, 2); Alin & Hopson (1992; Fig. 28.4c); Sigogneau & Tchudinov (1972, Figs. 1, 15). Eoarctops modified from Broom (1932, Fig. 35a); Boonstra (1969, Fig. 18). Pristerognathus modified from Broom (1932, Figs 17a, b,c); Boonstra (1963, Fig. 5d). Procynosuchus modified from Allin & Hopson (1992, Fig. 28.4e); Hopson (1987, Fig. 5c); Brink (1963, Fig. 10a); Kemp (1979, Fig. 1); Allin (1975, p. 3, Fig. 14). Thrinaxodon modified from Allin & Hopson (1992, Fig. 28.4f);Parrington (1946, Fig. 1); Allin (1975, p. 3, Fig. 13). Probainognathus modified from Allin & Hopson (1992, Fig. 28.4g); Romer (1970, Fig. 1); Allin (1975, p. 3, Fig. 12). Morga nucodon modified from Kermack, Mussett, & Rigney (1981, Figs. 95, 99a; 1973, Fig. 7a); Allin (1975, p. 3, Fig. 11). Asioryctes modified from Carroll (1988, Fig. 20-3b). Abbreviations: ag = angular; ar = articular; cp = coronoid process; d = dentary; f = lateral temporal fenestra; j = jugal; mm = attachment site for mammalian jaw muscles; o = eye socket; po = post orbital; q = quadrate; rl = reflected lamina; sq = squamosal; ty = tympanic.

M: Early Placental mammals
Upper Cretaceous
Merged with eye socket; cheek arch bowed out laterally 100% of jaw length is the den- tary; condylar process in contact with squamosal Fully differentiated teeth; incisors, canines, premolars; one tooth replacement No post-dentary bones 3 middle ear bones (stapes, incus, malleus) + tympanic; squamosal-dentary jaw joint
L: "Pantothere" mammals
Middle/Upper Jurassic
X 100% of jaw length is the den-  tary; condylar process contacts squamosal Fully differentiated teeth; incisors, canines, premolars; one tooth replacement Post-dentary bones migrated to middle ear Probably 3 middle ear bones (stapes, incus, malleus) + tympanic; squamosal-dentary jaw joint
K: Morganucodontid mammals
Morganucodon  Upper Triassic & Lower Jurassic
Merged with eye socket; cheeck arch bowed out laterally 100% of jaw length is the den- tary; condylar process expanded posteriorly to make contact with squamosal Fully differentiated teeth; incisors, canines, premolars; one tooth replacement 20% of jaw length; reflected lamina decreased to narrow ribbon-like horseshoe Stapes extends from inner ear capsule to quadrate; quadrate tiny; both quadrate-articular and squamosal-dentary jaw joints
J: Chiniquodontid cynodonts
Middle Triassic
Much larger than eye socket; 40- 45% of skull length; expanded posterioirly, medially, & laterally; midline of skull narrow sagittal crest; chek arch bowed out laterally 95% of jaw length is the dentary; large coronoid process expanded posteriorly; condylar process expanded posteriorly Large single canine; cheek teeth multicusped; tooth replacement reduced 20% of jaw length; angular notch widened ventrally; width of main part of angular decreased; reflec - ted lamina decreased to narrow ribbon-like horseshoe Stapes extends from inner ear capsule to quadrate; quadrate tiny; quadrate-articular joint
I:Galesaurid cynodonts
Lower Triassic
Much larger than eye socket; 40% of skull length; expanded pos- terioirly, medially, & laterally; midline of skull narrow sagittal crest; chek arch bowed out laterally 85% of jaw length is the dentary; large coronoid process expanded to top of eye socket and pos- teriorly; jaw muscles attached to most of coronoid process Large single canine; cheek teeth multicusped; tooth replacement reduced 25% of jaw length; angular notch widened ventrally; width of reflec- ted lamina decreased; width of main part of angular decreased Stapes extends from inner ear capsule to quadrate; quadrate small; quadrate-articular jaw joint
H: Procynosuchid cynodonts
upper Upper Permian
Much larger than eye socket; 40% of skull length; expanded pos- terioirly, medially, & laterally; midline of skull narrow sagittal crest; chek arch bowed out laterally 75-80% of jaw length is the den- tary; coronoid process expanded to near top of eye socket and posteriorly; jaw muscles  attached to dorsal part of coronoid process Large single canine; cheek teeth multicusped 30% of jaw length; angular notch widened ventrally; width of reflected lamina decreased Stapes extends from inner ear capsule to quadrate; quadrate small; quadrate-articular jaw joint
G: Early Therocephalians
lower Upper Permian
Larger than eye socket; expanded posteriorly and medially; 30% of skull length 75-80% of jaw length is the den- tary; posterior end of dentary expanded posteriorly and dorsally into narrow blade-like coronoid process; rises to middle of eye socket Large single canine; other teeth simple cones. 35% of jaw length; angular notch deepened into a cleft; reflected lamina large, broad, blade-like Stapes extends from inner ear capsule to quadrate; quadrate small; quadrate-articular jaw joint
F: Early Gorgonopsians
lower Upper Permian
Slightly larger than eye socket; expanded posteriorly and medially (minimal); 20-25% of skull length 65-75% of jaw length is the den- tary; posterior end of dentary slightly expanded posteriorly and dorsally as incipient coronoid process Large single canine; other teeth simple cones. 40% of jaw length; angular notch deepened into a cleft; reflected lamina large, broad, blade-like Stapes extends from inner ear capsule to quadrate; quadrate- articular jaw joint
E: Eotitanosuchians
Lower Permian
Small; slightly smaller than eye socket; slightly expanded posteriorly and medially 65-75% of jaw length is the den- tary; posterodorsal edge rises broadly but slightly above tooth row Large single canine; other teeth simple cones. 40% of jaw length; angular notch deepened into a cleft; reflected lamina large, broad, blade-like Stapes extends from inner ear capsule to quadrate;  quadrate- articular jaw joint 
D: Late sphenacodonts
Upper Pennsylvanian
Small; smaller than eye socket; confined to one side of skull 65% of jaw length is the dentary; posterodorsal edge rises broadly but slightly above the tooth row Enlarged incipient canines; other teeth simple cones 60% of jaw length; venntral edge of angular notched ("angular notch") offsetting a short pro- tusion (reflected lamina) Stapes extends from inner ear capsule to quadrate; quadrate large and plate-like; quadrate- articular jaw joint
C: Early spenacodonts
Upper Pennsylvanian
Tiny; smaller than eye socket; confined to one side of skull 65-75% of jaw length is the den- tary; posterodorsal edge rises broadly but slightly above tooth row Undifferentiated; slightly enlarged incipient canines just behind nares 70% of jaw length; ventral edge of angular with shallow indentation Stapes extends from inner ear capsule to quadrate; quadrate- articular jaw joint
B: Early ophiacodonts
upper Middle Pennsylvanian
Tiny; smaller than eye socket; confined to one side of skull x Undifferentiated; slightly enlarged incipient canines just behind nares x Stapes extends from inner ear capsule to quadrate; quadrate- articular jaw joint
A: Protorothyrids
lower Middle Pennsylvanian
Absent 65-75% of jaw length is the den- tary; posterodorsal edge rises broadly but slightly above tooth row Undifferentiated; slightly enlarged incipient canines just behind nares 70% of jaw length; ventral edge of angular continuous  Stapes extends from inner ear capsule to quadrate; quadrate- articular jaw joint

Table 1: Morphology of synapsid reptiles and mammals (Note that Hylonomus is a protothyrid, not a synapsid). Data from references cited in text.

Modern reptiles and mammals are very distinctive, easily diagnosable, and do not intergrade. Reptiles are covered by scales, mammals by hair; reptiles are cold-blooded, mammals warm-blooded; reptiles do not suckle their young, mammals have mammary glands; reptiles have sprawling posture, mammals have upright posture. Most of these features are soft part anatomy or physiology that very rarely fossilize (although dinosaur skin impressions are known from Cretaceous sediments, and imprints of mammal hair are known from Eocene bats from Germany; Franzen, 1990). In the fossil record, we must look to skeletal features.

There are many skeletal features which allow us to distinguish the reptiles from the mammals (Carroll, 1988; Table 1, rows A, M). The single most important defining characteristic is the nature of the articulation of the lower jaw to the skull (Simpson, 1959). In reptiles, multiple bones comprise the lower jaw. A small bone at the posterior end of the lower jaw, the articular, articulates with the quadrate bone of the skull (Simpson, 1959; Carroll, 1988). In mammals, one large bone, the dentary, comprises the lower jaw. It articulates with the squamosal bone of the skull (Simpson, 1959; Carroll, 1988).

From comparative anatomy studies, it is certain that most of the bones of the reptiles and mammals are homologous (Crompton & Parker, 1978; Carroll, 1988). Of greatest importance, the middle ear bones of mammals (stapes, incus, malleus, and tympanic) are homologous with several of the skull and jaw bones of reptiles (stapes, quadrate, articular, and angular, respectively; Romer, 1956, p. 33-38, 1970a; Allin, 1975, 1986; Allin & Hopson, 1992; Crompton & Parker, 1978; Hopso n, 1987, 1994; Carroll, 1988). One group of reptiles, the synapsids (Subclass Synapsida), share with the mammals an additional homologous structure: the lateral temporal fenestra, which is an opening in the skull behind the eye socket at the triple junction between the squamosal, jugal , and post orbital bones (Broom, 1932; Frazetta, 1968; Kemp, 1982; Carroll, 1988). A band of bone composed of the jugal and the squamosal is adjacent to the lateral temporal fenestra (Broom, 1932; Kemp, 1982; Carroll, 1988). This is the cheek arch so characteristic of mammal skulls (Broom, 1932; Kemp, 1982; Carroll, 1988). Therefore, synapsids are commonly named the “mammal-like reptiles.”

The presence of diagnosable morphologic differences between reptiles (including the oldest reptiles and the oldest synapsids) and mammals distinguishes them as distinct taxa. This allows us to test evolution by looking for transitional forms between the two. Because many of the bones are homologous, we should find evidence illustrating how these bones were modified over time to become the new bones. Furthermore, these morphologic changes should happen in parallel and in geochronologic succession.

Synapsid reptiles inhabited Pangea from the Middle Pennsylvanian through the Early Jurassic (Kemp, 1982, 1985; Sloan, 1983; Carroll, 1988; Hopson, 1969, 1987, 1994; Hopson & Crompton, 1969; Hotton, et al., 1986; Crompton & Jenkins, 1973; Sidor & Hopson, 1998; Romer & Price, 1940; Broom, 1932; Boonstra, 1963, 1969, 1971; Tchudinov, 1983; Olson, 1944; Tatarinov, 1974; Vyushkov, 1955; Efremov, 1954). From the Early Permian through the Early Triassic, they were the largest and most abundant land animals (Sloan, 1983; Colbert, 1965). Though much less well known to the general public than dinosaurs, one of the “cereal box dinosaurs,” Dimetrodon (the sail-backed reptile), is a synapsid, not a dinosaur (Romer & Price, 1940; Carroll, 1988). The oldest mammals are Late Triassic (Kemp, 1982; Carroll, 1988). Below is a discussion of the geochronologic succession linking synapsids and mammals. The oldest reptiles (named protorothyrids; Carroll, 1964, 1988, p. 192-199) are from the lower Middle Pennsylvanian, and the oldest synapsids (Reisz, 1972) are from the upper Middle Pennsylvanian, both of Nova Scotia. Upper Pennsylvanian and Lower Permian forms are known primarily from the midcontinent and Permian Basin region of the United States (Romer & Price, 1940; Currie, 1977, 1979; Kemp, 1982; Sloan, 1983). The basal Upper Permian forms are known from Russia (Tchudinov, 1960, 1983; Efremov, 1954; Olson, 1962; Sigogneau & Tchudinov, 1972; Ivakhnenko et al., 1997). Most of the Upper Permian and Lower Triassic succession is known from southern Africa, especially the Great Karoo of South Africa (Broom, 1932; Boonstra, 1963, 1969, 1971; Hopson & Kitching, 1972; Kemp, 1982; Sloan, 1983). The Middle Triassic forms are from South America (Romer, 1969a, 1969b, 1970b, 1973; Romer & Lewis, 1973; Bonaparte & Barbarena, 1975), and the Upper Triassic and Lower Jurassic mammals are known from Eurasia (Kermack, Mussett, & Rigney, 1973, 1981; Kemp, 1982). Subsequent Mesozoic mammals are known from all over the world (Simpson, 1928; Lillegraven et al., 1979).

When placed in proper geochronologic succession, the synapsids naturally form a succession of taxa (genera and families) that progressively become more mammal-like and less reptile-like (Kemp, 1982, 1985; Sloan, 1983; Sidor & Hopson, 1998; Hopson, 1987, 1994). Morphologic changes, summarized in Table 1 and Figure 1, affect the entire skeletal anatomy of these animals, but are most clearly displayed in their skulls.

The lateral temporal fenestra increased in size from a tiny opening smaller than the eye socket to a giant opening occupying nearly half the length of the skull. Ultimately, it merged with the eye socket, thus producing the full development of the cheek arch so characteristic of mammals (Broom, 1932; Frazetta, 1968; Kemp, 1982; Sloan, 1983; Hopson, 1987, 1994; Carroll, 1988).

Successively, the relative proportion of the lower jaw comprised of the dentary bone (teeth-bearing bone) gradually increased until the entire lower jaw consisted of the dentary (Kemp, 1982; Sloan, 1983; Carroll, 1988; Hopson, 1987, 1994). In Pennsylvanian and Lower and basal Upper Permian synapsids, the postero-dorsal edge of the lower jaw rose broadly but only slightly above the level of the tooth row (Romer & Price, 1940; Currie, 1977, 1979; Ivakhnenko et al., 1997; Tchudinov, 1960, 1983; Efremov, 1954; Olson, 1962; Sigogneau & Tchudinov, 1972; Hopson, 1987, 1994). In succeeding forms, the posterior part of the dentary expanded dorsally and posteriorly as a blade-like process, and progressively became larger (Broom, 1932; Boonstra, 1963, 1969, 1971; Sigogneau, 1970; Brink, 1963; Kemp, 1979; Hopson, 1987, 1994), forming the coronoid process (Parrington, 1946; Fourie, 1974; Romer, 1969b, 1970b, 1973; Hopson, 1987, 1994) to which the mammalian-type jaw musculature is attached (Barghusen, 1968; Bramble, 1978; Crompton, 1972; Crompton & Parker, 1978; Kemp, 1982; Sloan, 1983; Carroll, 1988). Concomitantly, the post-dentary bones progressively reduced in size (Allin, 1975; Crompton, 1972; Crompton & Parker, 1978; Kemp, 1982; Sloan, 1983; Carroll, 1988; Hopson, 1987, 1994).

Beginning with the Upper Pennsylvanian sphenacodonts, a notch developed in the angular bone that offsets a projection, the reflected lamina (Allin, 1975; Allin & Hopson, 1992; Hopson, 1987, 1994; Romer & Price, 1940; Currie, 1977, 1979; Kemp, 1982; Sloan, 1983; Carroll, 1988). The reflected lamina first became a large blade-like flange (Allin, 1975; Allin & Hopson, 1992; Hopson, 1987, 1994; Ivakhnenko et al., 1997; Tchudinov, 1960, 1983; Efremov, 1954; Olson, 1962; Sigogneau & Tchudinov, 1972; Broom, 1932; Sigogneau, 1970; Boonstra, 1963, 1969, 1971), and then was progressively reduced to a delicate horseshoe-shaped bone (Allin, 1975; Allin & Hopson, 1992; Hopson, 1987, 1994; Brink, 1963; Parrington, 1946; Fourie, 1974; Romer, 1969b, 1970b, 1973; Kermack, Mussett, & Rigney, 1973, 1981; Kemp, 1979, 1982; Sloan, 1983; Carroll, 1988).

Simultaneously, the quadrate progressively decreased in size (Allin, 1975; Allin & Hopson, 1992; Hopson, 1987, 1994; Kemp, 1982; Sloan, 1983; Carroll, 1988). The articular did not decrease in size much, being small initially, but developed a downward-pointing prong (Allin, 1975; Allin & Hopson, 1992; Hopson, 1987, 1994; Kemp, 1982; Sloan, 1983; Carroll, 1988). In the synapsids, the lower jaw was hinged to the skull by the articular and quadrate bones (Crompton, 1972; Crompton & Parker, 1978; Allin, 1975; Allin & Hopson, 1992; Hopson, 1987, 1994). Thus they are classified as reptiles (Simpson, 1959; Kemp, 1982; Sloan, 1983; Carroll, 1988). As the quadrate and articular became smaller, they were relieved of their solid suture to the dentary and skull (Crompton, 1972; Allin, 1975, 1986; Allin & Hopson, 1992; Hopson, 1987, 1994; Crompton & Parker, 1978; Kemp, 1982; Sloan, 1983; Carroll, 1988). A projection of the dentary extended posteriorly and made contact with the squamosal. Morganucodon possessed the mammalian dentary-squamosal jaw joint adjacent to the reptilian articular-quadrate jaw joint (Kermack, Mussett, & Rigney, 1973, 1981; Carroll, 1988). It is classified as the first mammal, but it is a perfect intermediate. Now that a new jaw joint was established, the quadrate and articular were subsequently relieved of that function (Crompton, 1972; Allin, 1975, 1986; Allin & Hopson, 1992; Hopson, 1987, 1994; Crompton & Parker, 1978; Kemp, 1982; Sloan, 1983; Carroll, 1988). Ultimately, in Middle and Upper Jurassic mammals, the tiny quadrate, articular, and ring-like angular migrated as a unit to the middle ear where they joined the stapes and became the incus, malleus, and tympanic bones (Allin, 197 5, 1986; Allin & Hopson, 1992; Hopson, 1987, 1994; Kemp, 1982; Sloan, 1983; Carroll, 1988).

Progressively, the teeth became differentiated. The large canines developed first, followed by the development of multicusped cheek teeth, reduced tooth replacement (Osborn & Crompton, 1973; Crompton & Parker, 1978), and finally full y differentiated incisors, canines, premolars, and molars with one tooth replacement during life (Kemp, 1982; Hopson, 1994).

Many other morphologic changes are documented in the fossil record. These demonstrate the morphologic and geochronologic succession from sprawling limb posture to upright limb posture of mammals (Jenkins, 1971; Romer & Lewis, 197 3; Kemp, 1982; Carroll, 1988; Hopson, 1994). As Jenkins (1971, p. 210) stated, “In details of morphology and function, the cynodont post-cranial skeleton should be regarded as neither ‘reptilian’ nor ‘mammalian’ but as transitional between the two classes .” Other changes have been adequately summarized elsewhere (Kemp, 1982; Sloan, 1983; Carroll, 1988; Hopson, 1994). Obviously, fundamental physiologic changes must have taken place as well, many of which are not directly preserved in the fossil record, though some can be inferred from the skeletal anatomy (Findlay, 1968; Kemp, 1982; Sloan, 1983, Carroll, 1988; Hopson, 1994).

This is well documented in the fossil record by a massive volume of incontrovertible data that cannot be explained away. Such large-scale, progressive, continuous, gradual, and geochronologically successive morphologic change (Sidor & Hopson, 1998) is descent with modification, and provides compelling evidence for evolution on a grand scale.

(The above is from The Fossil Record: Evolution or "Scientific Creation", which is yet ANOTHER source the anti-evolutionists are obviously completely ignorant of -- not that that stops them from spouting off falsehoods about the subject anyway...

Theropod dinosaur to bird evolutionary transition:

The cladogram for the evolution of flight looks like this:

Image Hosted by

(Note -- each name along the top is a known transitional fossil; and those aren't all that have been discovered.) Here's a more detailed look at the middle section:

Image Hosted by

Fossils discovered in the past ten years in China have answered most of the "which came first" questions about the evolution of birds from dinosaurs.

We now know that downy feathers came first, as seen in this fossil of Sinosauropteryx:

Image Hosted by

That's a close-up of downy plumage along the backbone. Here's a shot of an entire fossil

Image Hosted by

Sinosauropteryx was reptilian in every way, not counting the feathers. It had short forelimbs, and the feathers were all the same size. Presumably, the downy feathers evolved from scales driven by a need for bodily insulation.

Next came Protarchaeopteryx:

Image Hosted by

It had long arms, broad "hands", and long claws:

Image Hosted by

Apparently this species was driven by selection to develop more efficient limbs for grasping prey. One of the interesting things about this species is that the structure of the forelimb has been refined to be quite efficient at sweeping out quickly to grab prey, snap the hands together, then draw them back towards the body (mouth?). The specific structures in question are the semilunate carpal (a wrist bone), that moves with the hand in a broad, flat, 190 degree arc, heavy chest muscles, bones of the arm which link together with the wrist so as to force the grasping hands to spread out toward the prey during the forestroke and fold in on the prey during the upstroke. Not only is this a marvelously efficient prey-grabbing mechanism, but the same mechanism is at the root of the wing flight-stroke of modern birds. Evolution often ends up developing a structure to serve one need, then finds it suitable for adaptation to another. Here, a prey-grasping motion similar in concept to the strike of a praying mantis in a reptile becomes suitable for modifying into a flapping flight motion.

Additionally, the feathers on the hands and tail have elongated, becoming better suited for helping to sweep prey into the hands.

Next is Caudipteryx:

Image Hosted by

This species had hand and tail feathers even more developed than the previous species, and longer feathers, more like that of modern birds:

Image Hosted by

However, it is clear that this was still not a free-flying animal yet, because the forelimbs were too short and the feathers not long enough to support its weight, and the feathers were symmetrical (equal sized "fins" on each side of the central quill). It also had very reduced teeth compared to earlier specimens and a stubby beak:

Image Hosted by

But the elongation of the feathers indicates some aerodynamic purpose, presumably gliding after leaping (or falling) from trees which it had climbed with its clawed limbs, in the manner of a flying squirrel. Feathers which were developed "for" heat retention and then pressed into service to help scoop prey were now "found" to be useful for breaking falls or gliding to cover distance (or swooping down on prey?).

Next is Sinornithosaurus:

Similar to the preceding species, except that the pubis bone has now shifted to point to the back instead of the front, a key feature in modern birds (when compared to the forward-facing publis bone in reptiles). Here are some of the forearm feathers in detail:

Long feathers in detail:

Artists' reconstruction:

Next is Archaeopteryx:

The transition to flight is now well underway. Archaeopteryx has the reversed hallux (thumb) characteristic of modern birds, and fully developed feathers of the type used for flight (long, aligned with each other, and assymetrical indicating that the feathers have been refined to function aerodynamically). The feathers and limbs are easily long enough to support the weight of this species in flight. However, it lacks some structures which would make endurance flying more practical (such as a keeled sternum for efficient anchoring of the pectoral muscles which power the downstroke) and fused chest vertebrae. Archaeopteryx also retains a number of clearly reptilian features still, including a clawed "hand" emerging from the wings, small reptilian teeth, and a long bony tail. After the previous species' gliding abilities gave it an advantage, evolution would have strongly selected for more improvements in "flying" ability, pushing the species towards something more resembling sustained powered flight.

Next is Confuciusornis:

Image Hosted by

This species had a nearly modern flight apparatus. It also displays transitional traits between a reptilian grasping "hand" and a fully formed wing as in modern birds -- the outer two digits (the earlier species had three-fingered "hands") in Confuciusornis are still free, but the center digit has now formed flat, broad bones as seen in the wings of modern birds.

Image Hosted by

Additionally, the foot is now well on its way towards being a perching foot as in modern birds:

Image Hosted by

It also has a keeled sternum better suited for long flight, and a reduced number of vertebrae in the tail, on its way towards becoming the truncated tail of modern birds (which while prominent, is a small flap of muscle made to look large only because of the long feathers attached).

From this species it's only a small number of minor changes to finish the transition into the modern bird family.

(Hey, who said there are no transitional fossils? Oh, right, a lot of dishonest creationists. And there are a lot more than this, I've just posted some of the more significant milestones.)

There's been a very recent fossil find along this same lineage, too new for me to have found any online images to include in this article. And analysis is still underway to determine exactly where it fits into the above lineage. But it has well-formed feathers, which extend out from both the "arms" and the legs. Although it wasn't advanced enough to fully fly, the balanced feathering on the front and back would have made it ideally suited for gliding like a flying squirrel, and it may be another link between the stage where feathers had not yet been pressed into service as aerodynamic aids, and the time when they began to be used more and more to catch the air and developing towards a "forelimbs as wings" specialization.

So in short, to answer your question about how flight could have developed in birds, the progression is most likely some minor refinement on the following:

1. Scales modified into downy feathers for heat retention.
2. Downy feathers modified into "straight" feathers for better heat retention (modern birds still use their body "contour feathers" in this fashion).
3. Straight feathers modified into a "grasping basket" on the hands (with an accompanying increase in reach for the same purpose).
4. Long limbs with long feathers refined to better survive falls to the ground.
5. "Parachute" feathers refined for better control, leading to gliding.
6. Gliding refined into better controlled, longer gliding.
7. Long gliding refined into short powered "hops".
8. Short powered flight refined into longer powered flight.
9. Longer powered flight refined into long-distance flying.

Note that in each stage, the current configuration has already set the stage for natural selection to "prefer" individuals which better meet the requirements of the next stage. Evolution most often works like this; by taking some pre-existing ability or structure, and finding a better use for it or a better way to make it perform its current use.

Fish to elephant evolutionary transition

Tell me, of any two consecutive fossils in the following list, do any differ so much from each other that anti-evolutionists wouldn't just write it off as "just adaptation", or "just microevolution"? [All of the listed specimens are actual fossils]

Fish to Amphibian transition:

1. Cheirolepis, (early Devonian, 400 million years ago) -- Primitive bony ray-finned fishes that gave rise to the vast majority of living fish. Heavy acanthodian-type scales, acanthodian-like skull, and big notocord.

2. Osteolepis (mid-Devonian, 390 million years ago) -- One of the earliest crossopterygian lobe-finned fishes, still sharing some characters with the lungfish (the other lobe-finned fishes). Had paired fins with a leg-like arrangement of major limb bones, capable of flexing at the "elbow", and had an early-amphibian-like skull and teeth.

3. Eusthenopteron, Sterropterygion (mid-late Devonian, 380 million years ago) -- Early rhipidistian lobe-finned fish roughly intermediate between early crossopterygian fish and the earliest amphibians. Skull very amphibian-like. Strong amphibian- like backbone. Fins very like early amphibian feet in the overall layout of the major bones, muscle attachments, and bone processes, with tetrapod-like tetrahedral humerus, and tetrapod-like elbow and knee joints. But there are no perceptible "toes", just a set of identical fin rays. Body & skull proportions rather fishlike.

4. Panderichthys, Elpistostege (mid-late Devonian, about 370 Mya) -- These "panderichthyids" are very tetrapod-like lobe-finned fish. Unlike Eusthenopteron, these fish actually look like tetrapods in overall proportions (flattened bodies, dorsally placed orbits, frontal bones! in the skull, straight tails, etc.) and have remarkably foot-like fins.

5. Obruchevichthys(middle Late Devonian, about 370 Mya -- Discovered in 1991 in Scotland, these are the earliest known tetrapod remains. The humerus is mostly tetrapod-like but retains some fish features. The discoverer, Ahlberg (1991), said: "It [the humerus] is more tetrapod-like than any fish humerus, but lacks the characteristic early tetrapod 'L-shape'...this seems to be a primitive, fish-like character....although the tibia clearly belongs to a leg, the humerus differs enough from the early tetrapod pattern to make it uncertain whether the appendage carried digits or a fin. At first sight the combination of two such extremities in the same animal seems highly unlikely on functional grounds. If, however, tetrapod limbs evolved for aquatic rather than terrestrial locomotion, as recently suggested, such a morphology might be perfectly workable."

6. Hynerpeton, Acanthostega, Ichthyostega (late Devonian, 360 Mya) -- A little later, the fin-to-foot transition was almost complete, and we have a set of early tetrapod fossils that clearly did have feet. The most complete are Ichthyostega, Acanthostega gunnari, and the newly described Hynerpeton bassetti (Daeschler et al., 1994). (There are also other genera known from more fragmentary fossils.) Hynerpeton is the earliest of these three genera (365 Ma), but is more advanced in some ways; the other two genera retained more fish- like characters longer than the Hynerpeton lineage did. Acanthostega still had internal gills, adding further support to the suggestion that unique tetrapod characters such as limbs with digits evolved first for use in water rather than for walking on land. Acanthostega also had a remarkably fish-like shoulder and forelimb. Ichthyostega was also very fishlike, retaining a fish-like finned tail, permanent lateral line system, and notochord. It turns out that Acanthostega's front foot had eight toes, and Ichthyostega's hind foot had seven toes, giving both feet the look of a short, stout flipper with many "toe rays" similar to fin rays. All you have to do to a lobe- fin to make it into a many-toed foot like this is curl it, wrapping the fin rays forward around the end of the limb. In fact, this is exactly how feet develop in larval amphibians, from a curled limb bud. Hynerpeton, in contrast, probably did not have internal gills and already had a well-developed shoulder girdle; it could elevate and retract its forelimb strongly, and it had strong muscles that attached the shoulder to the rest of the body (Daeschler et al., 1994).

7. Labyrinthodonts (eg Pholidogaster, Pteroplax) (late Dev./early Miss., 355 Mya) -- These larger amphibians still have some icthyostegid fish features, such as skull bone patterns, labyrinthine tooth dentine, presence & pattern of large palatal tusks, the fish skull hinge, pieces of gill structure between cheek & shoulder, and the vertebral structure. But they have lost several other fish features: the fin rays in the tail are gone, the vertebrae are stronger and interlocking, the nasal passage for air intake is well defined, etc.

Amphibian to Reptile transition:

8. Pholidogaster (Mississippian, about 330 Ma) -- A group of large labrinthodont amphibians, transitional between the early amphibians (the ichthyostegids, described above) and later amphibians such as rhachitomes and anthracosaurs.

9. Proterogyrinus (late Mississippian, 325 Mya) -- Classic labyrinthodont-amphibian skull and teeth, but with reptilian vertebrae, pelvis, humerus, and digits. Still has fish skull hinge. Amphibian ankle. 5-toed hand and a 2-3-4-5-3 (almost reptilian) phalangeal count.

10. Limnoscelis, Tseajaia (late Carboniferous, 300 Mya) -- Amphibians apparently derived from the early anthracosaurs, but with additional reptilian features: structure of braincase, reptilian jaw muscle, expanded neural arches.

11. Solenodonsaurus (mid-Pennsylvanian) -- An incomplete fossil, apparently between the anthracosaurs and the cotylosaurs. Loss of palatal fangs, loss of lateral line on head, etc. Still just a single sacral vertebra, though.

12. Hylonomus, Paleothyris (early Pennsylvanian) -- These are protorothyrids, very early cotylosaurs (primitive reptiles). They were quite little, lizard-sized animals with amphibian-like skulls (amphibian pineal opening, dermal bone, etc.), shoulder, pelvis, & limbs, and intermediate teeth and vertebrae. Rest of skeleton reptilian, with reptilian jaw muscle, no palatal fangs, and spool-shaped vertebral centra. Probably no eardrum yet.

13. Paleothyris (early Pennsylvanian) -- An early captorhinomorph reptile, with no temporal fenestrae at all.

14. Protoclepsydrops haplous (early Pennsylvanian) -- The earliest known synapsid reptile. Little temporal fenestra, with all surrounding bones intact. Had amphibian-type vertebrae with tiny neural processes. (reptiles had only just separated from the amphibians)

15. Clepsydrops (early Pennsylvanian) -- The second earliest known synapsid.

Reptile to Mammal transition:

16. Archaeothyris (early-mid Pennsylvanian) -- A slightly later ophiacodont. Small temporal fenestra, now with some reduced bones (supratemporal). Braincase still just loosely attached to skull. Slight hint of different tooth types. Still has some extremely primitive, amphibian/captorhinid features in the jaw, foot, and skull. Limbs, posture, etc. typically reptilian, though the ilium (major hip bone) was slightly enlarged.

17. Varanops (early Permian) -- Temporal fenestra further enlarged. Braincase floor shows first mammalian tendencies & first signs of stronger attachment to rest of skull (occiput more strongly attached). Lower jaw shows first changes in jaw musculature (slight coronoid eminence). Body narrower, deeper: vertebral column more strongly constructed. Ilium further enlarged, lower-limb musculature starts to change (prominent fourth trochanter on femur). This animal was more mobile and active. Too late to be a true ancestor, and must be a "cousin".

18. Haptodus (late Pennsylvanian) -- One of the first known sphenacodonts, showing the initiation of sphenacodont features while retaining many primitive features of the ophiacodonts. Occiput still more strongly attached to the braincase. Teeth become size-differentiated, with biggest teeth in canine region and fewer teeth overall. Stronger jaw muscles. Vertebrae parts & joints more mammalian. Neural spines on vertebrae longer. Hip strengthened by fusing to three sacral vertebrae instead of just two. Limbs very well developed.

19. Dimetrodon, Sphenacodon or a similar sphenacodont (late Pennsylvanian to early Permian, 270 Ma) -- More advanced pelycosaurs, clearly closely related to the first therapsids (next). Dimetrodon is almost definitely a "cousin" and not a direct ancestor, but as it is known from very complete fossils, it's a good model for sphenacodont anatomy. Medium-sized fenestra. Teeth further differentiated, with small incisors, two huge deep- rooted upper canines on each side, followed by smaller cheek teeth, all replaced continuously. Fully reptilian jaw hinge. Lower jaw bone made of multiple bones & with first signs of a bony prong later involved in the eardrum, but there was no eardrum yet, so these reptiles could only hear ground-borne vibrations (they did have a reptilian middle ear). Vertebrae had still longer neural spines (spectacularly so in Dimetrodon, which had a sail), and longer transverse spines for stronger locomotion muscles.

20. Biarmosuchia (late Permian) -- A therocephalian -- one of the earliest, most primitive therapsids. Several primitive, sphenacodontid features retained: jaw muscles inside the skull, platelike occiput, palatal teeth. New features: Temporal fenestra further enlarged, occupying virtually all of the cheek, with the supratemporal bone completely gone. Occipital plate slanted slightly backwards rather than forwards as in pelycosaurs, and attached still more strongly to the braincase. Upper jaw bone (maxillary) expanded to separate lacrymal from nasal bones, intermediate between early reptiles and later mammals. Still no secondary palate, but the vomer bones of the palate developed a backward extension below the palatine bones. This is the first step toward a secondary palate, and with exactly the same pattern seen in cynodonts. Canine teeth larger, dominating the dentition. Variable tooth replacement: some therocephalians (e.g Scylacosaurus) had just one canine, like mammals, and stopped replacing the canine after reaching adult size. Jaw hinge more mammalian in position and shape, jaw musculature stronger (especially the mammalian jaw muscle). The amphibian-like hinged upper jaw finally became immovable. Vertebrae still sphenacodontid-like. Radical alteration in the method of locomotion, with a much more mobile forelimb, more upright hindlimb, & more mammalian femur & pelvis. Primitive sphenacodontid humerus. The toes were approaching equal length, as in mammals, with #toe bones varying from reptilian to mammalian. The neck & tail vertebrae became distinctly different from trunk vertebrae. Probably had an eardrum in the lower jaw, by the jaw hinge.

21. Procynosuchus (latest Permian) -- The first known cynodont -- a famous group of very mammal-like therapsid reptiles, sometimes considered to be the first mammals. Probably arose from the therocephalians, judging from the distinctive secondary palate and numerous other skull characters. Enormous temporal fossae for very strong jaw muscles, formed by just one of the reptilian jaw muscles, which has now become the mammalian masseter. The large fossae is now bounded only by the thin zygomatic arch (cheekbone to you & me). Secondary palate now composed mainly of palatine bones (mammalian), rather than vomers and maxilla as in older forms; it's still only a partial bony palate (completed in life with soft tissue). Lower incisor teeth was reduced to four (per side), instead of the previous six (early mammals had three). Dentary now is 3/4 of lower jaw; the other bones are now a small complex near the jaw hinge. Jaw hinge still reptilian. Vertebral column starts to look mammalian: first two vertebrae modified for head movements, and lumbar vertebrae start to lose ribs, the first sign of functional division into thoracic and lumbar regions. Scapula beginning to change shape. Further enlargement of the ilium and reduction of the pubis in the hip. A diaphragm may have been present.

22. Dvinia [also "Permocynodon"] (latest Permian) -- Another early cynodont. First signs of teeth that are more than simple stabbing points -- cheek teeth develop a tiny cusp. The temporal fenestra increased still further. Various changes in the floor of the braincase; enlarged brain. The dentary bone was now the major bone of the lower jaw. The other jaw bones that had been present in early reptiles were reduced to a complex of smaller bones near the jaw hinge. Single occipital condyle splitting into two surfaces. The postcranial skeleton of Dvinia is virtually unknown and it is not therefore certain whether the typical features found at the next level had already evolved by this one. Metabolic rate was probably increased, at least approaching homeothermy.

23. Thrinaxodon (early Triassic) -- A more advanced "galesaurid" cynodont. Further development of several of the cynodont features seen already. Temporal fenestra still larger, larger jaw muscle attachments. Bony secondary palate almost complete. Functional division of teeth: incisors (four uppers and three lowers), canines, and then 7-9 cheek teeth with cusps for chewing. The cheek teeth were all alike, though (no premolars & molars), did not occlude together, were all single- rooted, and were replaced throughout life in alternate waves. Dentary still larger, with the little quadrate and articular bones were loosely attached. The stapes now touched the inner side of the quadrate. First sign of the mammalian jaw hinge, a ligamentous connection between the lower jaw and the squamosal bone of the skull. The occipital condyle is now two slightly separated surfaces, though not separated as far as the mammalian double condyles. Vertebral connections more mammalian, and lumbar ribs reduced. Scapula shows development of a new mammalian shoulder muscle. Ilium increased again, and all four legs fully upright, not sprawling. Tail short, as is necessary for agile quadrupedal locomotion. The whole locomotion was more agile. Number of toe bones is, intermediate between reptile number ( and mammalian (, and the "extra" toe bones were tiny. Nearly complete skeletons of these animals have been found curled up - a possible reaction to conserve heat, indicating possible endothermy? Adults and juveniles have been found together, possibly a sign of parental care. The specialization of the lumbar area (e.g. reduction of ribs) is indicative of the presence of a diaphragm, needed for higher O2 intake and homeothermy. NOTE on hearing: The eardrum had developed in the only place available for it -- the lower jaw, right near the jaw hinge, supported by a wide prong (reflected lamina) of the angular bone. These animals could now hear airborne sound, transmitted through the eardrum to two small lower jaw bones, the articular and the quadrate, which contacted the stapes in the skull, which contacted the cochlea. Rather a roundabout system and sensitive to low-frequency sound only, but better than no eardrum at all! Cynodonts developed quite loose quadrates and articulars that could vibrate freely for sound transmittal while still functioning as a jaw joint, strengthened by the mammalian jaw joint right next to it. All early mammals from the Lower Jurassic have this low-frequency ear and a double jaw joint. By the middle Jurassic, mammals lost the reptilian joint (though it still occurs briefly in embryos) and the two bones moved into the nearby middle ear, became smaller, and became much more sensitive to high-frequency sounds.

24. Cynognathus (early Triassic, 240 Ma; suspected to have existed even earlier) -- We're now at advanced cynodont level. Temporal fenestra larger. Teeth differentiating further; cheek teeth with cusps met in true occlusion for slicing up food, rate of replacement reduced, with mammalian-style tooth roots (though single roots). Dentary still larger, forming 90% of the muscle-bearing part of the lower jaw. TWO JAW JOINTS in place, mammalian and reptilian: A new bony jaw joint existed between the squamosal (skull) and the surangular bone (lower jaw), while the other jaw joint bones were reduced to a compound rod lying in a trough in the dentary, close to the middle ear. Ribs more mammalian. Scapula halfway to the mammalian condition. Limbs were held under body. There is possible evidence for fur in fossil pawprints.

25. Diademodon (early Triassic, 240 Ma; same strata as Cynognathus) -- Temporal fenestra larger still, for still stronger jaw muscles. True bony secondary palate formed exactly as in mammals, but didn't extend quite as far back. Turbinate bones possibly present in the nose (warm-blooded?). Dental changes continue: rate of tooth replacement had decreased, cheek teeth have better cusps & consistent wear facets (better occlusion). Lower jaw almost entirely dentary, with tiny articular at the hinge. Still a double jaw joint. Ribs shorten suddenly in lumbar region, probably improving diaphragm function & locomotion. Mammalian toe bones (, with closely related species still showing variable numbers.

26. Probelesodon (mid-Triassic; South America) -- Fenestra very large, still separate from eyesocket (with postorbital bar). Secondary palate longer, but still not complete. Teeth double-rooted, as in mammals. Nares separated. Second jaw joint stronger. Lumbar ribs totally lost; thoracic ribs more mammalian, vertebral connections very mammalian. Hip & femur more mammalian.

27. Probainognathus (mid-Triassic, 239-235 Ma, Argentina) -- Larger brain with various skull changes: pineal foramen ("third eye") closes, fusion of some skull plates. Cheekbone slender, low down on the side of the eye socket. Postorbital bar still there. Additional cusps on cheek teeth. Still two jaw joints. Still had cervical ribs & lumbar ribs, but they were very short. Reptilian "costal plates" on thoracic ribs mostly lost. Mammalian #toe bones.

28. Pachygenelus, Diarthrognathus (earliest Jurassic, 209 Ma) -- These are trithelodontids. Inflation of nasal cavity, establishment of Eustachian tubes between ear and pharynx, loss of postorbital bar. Alternate replacement of mostly single- rooted teeth. This group also began to develop double tooth roots -- in Pachygenelus the single root of the cheek teeth begins to split in two at the base. Pachygenelus also has mammalian tooth enamel, and mammalian tooth occlusion. Double jaw joint, with the second joint now a dentary-squamosal (instead of surangular), fully mammalian. Incipient dentary condyle. Reptilian jaw joint still present but functioning almost entirely in hearing; postdentary bones further reduced to tiny rod of bones in jaw near middle ear; probably could hear high frequencies now. More mammalian neck vertebrae for a flexible neck. Hip more mammalian, with a very mammalian iliac blade & femur. Highly mobile, mammalian-style shoulder. Probably had coupled locomotion & breathing.

29. Sinoconodon (early Jurassic, 208 Ma) -- The next known very ancient proto-mammal. Eyesocket fully mammalian now (closed medial wall). Hindbrain expanded. Permanent cheekteeth, like mammals, but the other teeth were still replaced several times. Mammalian jaw joint stronger, with large dentary condyle fitting into a distinct fossa on the squamosal. This final refinement of the joint automatically makes this animal a true "mammal". Reptilian jaw joint still present, though tiny.

Proto-mammal to Placental Mammal transition:

30. Kuehneotherium (early Jurassic, about 205 Ma) -- A slightly later proto-mammal, sometimes considered the first known pantothere (primitive placental-type mammal). Teeth and skull like a placental mammal. The three major cusps on the upper & lower molars were rotated to form interlocking shearing triangles as in the more advanced placental mammals & marsupials. Still has a double jaw joint, though.

31. Eozostrodon, Morganucodon, Haldanodon (early Jurassic, ~205 Ma) -- A group of early proto-mammals called "morganucodonts". The restructuring of the secondary palate and the floor of the braincase had continued, and was now very mammalian. Truly mammalian teeth: the cheek teeth were finally differentiated into simple premolars and more complex molars, and teeth were replaced only once. Triangular- cusped molars. Reversal of the previous trend toward reduced incisors, with lower incisors increasing to four. Tiny remnant of the reptilian jaw joint. Once thought to be ancestral to monotremes only, but now thought to be ancestral to all three groups of modern mammals -- monotremes, marsupials, and placentals.

32. Peramus (late Jurassic, about 155 Ma) -- A "eupantothere" (more advanced placental-type mammal). The closest known relative of the placentals & marsupials. Triconodont molar has with more defined cusps. This fossil is known only from teeth, but judging from closely related eupantotheres (e.g. Amphitherium) it had finally lost the reptilian jaw joint, attaing a fully mammalian three-boned middle ear with excellent high-frequency hearing. Has only 8 cheek teeth, less than other eupantotheres and close to the 7 of the first placental mammals. Also has a large talonid on its "tribosphenic" molars, almost as large as that of the first placentals -- the first development of grinding capability.

33. Endotherium (very latest Jurassic, 147 Ma) -- An advanced eupantothere. Fully tribosphenic molars with a well- developed talonid. Known only from one specimen. From Asia; recent fossil finds in Asia suggest that the tribosphenic molar evolved there.

34. Vincelestes neuquenianus (early Cretaceous, 135 Ma) -- A probably-placental mammal with some marsupial traits, known from some nice skulls. Placental-type braincase and coiled cochlea. Its intracranial arteries & veins ran in a composite monotreme/placental pattern derived from homologous extracranial vessels in the cynodonts. (Rougier et al., 1992)

35. Kennalestes and Asioryctes (late Cretaceous, Mongolia) -- Small, slender animals; eyesocket open behind; simple ring to support eardrum; primitive placental-type brain with large olfactory bulbs; basic primitive tribosphenic tooth pattern. Canine now double rooted. Still just a trace of a non-dentary bone, the coronoid, on the otherwise all-dentary jaw. "Could have given rise to nearly all subsequent placentals." says Carroll (1988).

Placental mammal to elephant transition:

36. Protungulatum (latest Cretaceous) -- Transitional between earliest placental mammals and the condylarths (primitive, small hoofed animals). These early, simple insectivore- like small mammals had one new development: their cheek teeth had grinding surfaces instead of simple, pointed cusps. They were the first mammal herbivores. All their other features are generalized and primitive -- simple plantigrade five-toed clawed feet, all teeth present (3:1:4:3) with no gaps, all limb bones present and unfused, pointy-faced, narrow small brain, eyesocket not closed.

37. Minchenella or a similar condylarth (late Paleocene) -- Known only from lower jaws. Has a distinctive broadened shelf on the third molar.

38. Phenacolophus (late Paleocene or early Eocene) -- An early embrithopod (very early, slightly elephant-like condylarths), thought to be the stem-group of all elephants.

39. Pilgrimella (early Eocene) -- An anthracobunid (early proto-elephant condylarth), with massive molar cusps aligned in two transverse ridges.

40. Unnamed species of proto-elephant (early Eocene) -- Discovered recently in Algeria. Had slightly enlarged upper incisors (the beginnings of tusks), and various tooth reductions. Still had "normal" molars instead of the strange multi-layered molars of modern elephants. Had the high forehead and pneumatized skull bones of later elephants, and was clearly a heavy-boned, slow animal. Only one meter tall.

41. Moeritherium, Numidotherium, Barytherium (early-mid Eocene) -- A group of three similar very early elephants. It is unclear which of the three came first. Pig-sized with stout legs, broad spreading feet and flat hooves. Elephantish face with the eye set far forward & a very deep jaw. Second incisors enlarged into short tusks, in upper and lower jaws; little first incisors still present; loss of some teeth. No trunk.

42. Paleomastodon, Phiomia (early Oligocene) -- The first "mastodonts", a medium-sized animals with a trunk, long lower jaws, and short upper and lower tusks. Lost first incisors and canines. Molars still have heavy rounded cusps, with enamel bands becoming irregular. Phiomia was up to eight feet tall.

43. Gomphotherium (early Miocene) -- Basically a large edition of Phiomia, with tooth enamel bands becoming very irregular. Two long rows cusps on teeth became cross- crests when worn down. Gave rise to several families of elephant- relatives that spread all over the world. From here on the elephant lineages are known to the species level.

44a. The mastodon lineage split off here, becoming more adapted to a forest browser niche, and going through Miomastodon (Miocene) and Pliomastodon (Pliocene), to Mastodon (or "Mammut", Pleistocene).

44b. Meanwhile, the elephant lineage became still larger, adapting to a savannah/steppe grazer niche:

45. Stegotetrabelodon (late Miocene) -- One of the first of the "true" elephants, but still had two long rows of cross-crests, functional premolars, and lower tusks. Other early Miocene genera show compression of the molar cusps into plates (a modern feature ), with exactly as many plates as there were cusps. Molars start erupting from front to back, actually moving forward in the jaw throughout life.

46. Primelephas (latest Miocene) -- Short lower jaw makes it look like an elephant now. Reduction & loss of premolars. Very numerous plates on the molars, now; we're now at the modern elephants' bizarre system of one enormous multi-layered molar being functional at a time, moving forward in the jaw.

47. Primelephas gomphotheroides (mid-Pliocene) -- A later species that split into three lineages, Loxodonta, Elephas, and Mammuthus:

  1. Loxodonta adaurora (5 Ma). Gave rise to the modern African elephant Loxodonta africana about 3.5 Ma.
  2. Elephas ekorensis (5 Ma), an early Asian elephant with rather primitive molars, clearly derived directly from P. gomphotheroides. Led directly to:
    • Elephas recki, which sent off one side branch, E. hydrusicus, at 3.8 Ma, and then continued changing on its own until it became E. iolensis.
    • Elephas maximus, the modern Asian elephant, clearly derived from
    • E. hysudricus. Strikingly similar to young E. hysudricus animals. Possibly a case of neoteny (in which "new" traits are simply juvenile features retained into adulthood).
  3. Mammuthus meridionalis, clearly derived from P. gomphotheroides. Spread around the northern hemisphere. In Europe, led to M. armeniacus/trogontherii, and then to M. primigenius. In North America, led to M. imperator and then M. columbi.
The Pleistocene record for elephants is very good. In general, after the earliest forms of the three modern genera appeared, they show very smooth, continuous evolution with almost half of the speciation events preserved in fossils. For instance, Carroll (1988) says: "Within the genus Elephas, species demonstrate continuous change over a period of 4.5 million years. ...the elephants provide excellent evidence of significant morphological change within species, through species within genera, and through genera within a family...."

Species-species transitions among the elephants:

  • Maglio (1973) studied Pleistocene elephants closely. Overall, Maglio showed that at least 7 of the 17 Quaternary elephant species arose through smooth anagenesis transitions from their ancestors. For example, he said that Elephas recki "can be traced through a progressive series of stages...These stages pass almost imperceptibly into each other....In the late Pleistocene a more progressive elephant appears which I retain as a distinct species, E. iolensis, only as a matter of convenience. Although as a group, material referred to E. iolensis is distinct from that of E. recki, some intermediate specimens are known, and E. iolensis seems to represent a very progressive, terminal stage in the E. recki specific lineage."
  • Maglio also documented very smooth transitions between three Eurasian mammoth species: Mammuthus meridionalis --> M. armeniacus (or M. trogontherii) --> M. primigenius.
  • Lister (1993) reanalyzed mammoth teeth and confirmed Maglio's scheme of gradual evolution in European mammoths, and found evidence for gradual transitions in the North American mammoths too.
(Most of the above text is from The Transitional Vertebrate Fossils FAQ, and is the result of hard work by Kathleen Hunt, who deserves the credit. I've just extracted the relevant individual portions and assembled them into one direct fish-to-elephant sequence.) If you like that, here are a few hundred more.

Similar fossil sequences can be listed for the majority of other major-group transitions.

(Did I hear a creationist in the back row say something about "no transitional fossils?")

Note that the changes between any two sequential transitionals are small enough that most creationists would write them off as only "microevolution" -- and yet those 50-or-so "microevolutionary" steps turn a fish into an elephant, which even the most stubborn creationist would have to concede is "macroevolution".

Once you've answered the first question, here's a second one for you: If evolutionary common descent *hasn't* actually happened -- if the different animal "kinds" were just *poofed* into existence fully-formed -- then why is it possible to order known fossils into such a smooth "transitional" chain *at all*, in a way that makes sense and is chronologically, morphologically, genetically, paleontologically, geographically (etc. etc.) consistent with the (allegedly) "non-existent" evolutionary transitions? And no, it's not possible to assemble a sequence of fossils in just any damned order you want, so don't try *that* excuse -- even evolutionary biologists aren't capable of putting together a transitional fossil sequence "showing", say, a cat evolving into a bird, or a butterfly into a bat. Please explain.

Evolution of whales from terrestrial mammals

Links on whale evolution

(From Plagiarized Errors and Molecular Genetics)


A particularly impressive example of shared retroposons has recently been reported linking cetaceans (whales, dolphins and porpoises) to ruminants and hippopotamuses, and it is instructive to consider this example in some detail. Cetaceans are sea-living animals that bear important similarities to land-living mammals; in particular, the females have mammary glands and nurse their young. Scientists studying mammalian anatomy and physiology have demonstrated greatest similarities between cetaceans and the mammalian group known as artiodactyls (even-toed ungulates) including cows, sheep, camels and pigs. These observations have led to the evolutionist view that whales evolved from a four-legged artiodactyl ancestor that lived on land. Creationists have capitalized on the obvious differences between the familiar artiodactyls and whales, and have ridiculed the idea that whales could have had four-legged land-living ancestors. Creationists who claim that cetaceans did not arise from four-legged land mammals must ignore or somehow dismiss the fossil evidence of apparent whale ancestors looking exactly like one would predict for transitional species between land mammals and whales--with diminutive legs and with ear structures intermediate between those of modern artiodactyls and cetaceans (Nature 368:844,1994; Science 263: 210, 1994). (A discussion of fossil ancestral whale species with references may be found at Creationists must also ignore or dismiss the evidence showing the great similarity between cetacean and artiodactyl gene sequences (Molecular Biology & Evolution 11:357, 1994; ibid 13: 954, 1996; Gatesy et al, Systematic Biology 48:6, 1999).

Recently retroposon evidence has solidified the evolutionary relationship between whales and artiodactyls. Shimamura et al. (Nature 388:666, 1997; Mol Biol Evol 16: 1046, 1999; see also Lum et al., Mol Biol Evol 17:1417, 2000; Nikaido and Okada, Mamm Genome 11:1123, 2000) studied SINE sequences that are highly reduplicated in the DNA of all cetacean species examined. These SINES were also found to be present in the DNA of ruminants (including cows and sheep) but not in DNA of camels and pigs or more distantly related mammals such as horse, elephant, cat, human or kangaroo. These SINES apparently originated in a specific branch of ancestral artiodactyls after this branch diverged from camels, pigs and other mammals, but before the divergence of the lines leading to modern cetaceans, hippopotamus and ruminants. (See Figure 5.) In support of this scenario, Shimamura et al. identified two specific insertions of these SINES in whale DNA (insertions B and C in Figure 5) and showed that in DNA of hippopotamus, cow and sheep these same two sites contained the SINES; but in camel and pig DNA the same sites were "empty" of insertions. More recently, hippopotamus has been identified as the closest living terrestrial relative of cetaceans since hippos and whales share retroposon insertions (illustrated by D and E in Figure 5) that are not found in any other artiodactyls (Nikaido et al, PNAS 96:10261, 1999). The close hippo-whale relationship is consistent with previously reported sequence similarity comparisons (Gatesy, Mol Biol Evol 14:537, 1997) and with recent fossil finds (Gingerich et al., Science 293:2239, 2001; Thewissen et al., Nature 413:277, 2001) that resolve earlier paleontological conflicts with the close whale-hippo relationship. (Some readers have wondered: if ruminants are more closely related to whales than to pigs and camels, why are ruminants anatomically more similar to pigs and camels than they are to whales? Apparently this results from the fact that ruminants, pigs and camels changed relatively little since their last common ancestor, while the cetacean lineage changed dramatically in adapting to an aquatic lifestyle, thereby obliterating many of the features -- like hooves, fur and hind legs -- that are shared between its close ruminant relatives and the more distantly related pigs and camels. This scenario illustrates the fact that the rapid evolutionary development of adaptations to a new niche can occur through key functional mutations, leaving the bulk of the DNA relatively unchanged. The particularly close relationship between whales and hippos is consistent with several shared adaptations to aquatic life, including use of underwater vocalizations for communication and the absence of hair and sebaceous glands.) Thus, retroposon evidence strongly supports the derivation of whales from a common ancestor of hippopotamus and ruminants, consistent with the evolutionary interpretation of fossils and overall DNA sequence similarities. Indeed, the logic of the evidence from shared SINEs is so powerful that SINEs may be the best available characters for deducing species relatedness (Shedlock and Okada, Bioessays 22:148, 2000), even if they are not perfect (Myamoto, Curr. Biology 9:R816, 1999).

SINE insertions as tracers for phylogeny

Figure 5. Specific SINE insertions can act as "tracers" that illuminate phylogenetic relationships. This figure summarizes some of the data on SINEs found in living artiodactyls and shows how the shared insertions can be interpreted in relation to evolutionary branching. A specific SINE insertion event ("A" in the Figure) apparently occurred in a primitive common ancestor of pigs, ruminants, hippopotamus and cetaceans, since this insertion is present in these modern descendants of that common ancestor; but it is absent in camels, which split off from the other species before this SINE inserted. More recent insertions B and C are present only in ruminants, hippopotamus and cetaceans. Insertions D and E are shared only by hippopotamus and cetaceans, thereby identifying hippopotamus as the closest living relative of cetaceans (at least among the species examined in these studies). SINE insertions F and G occurred in the ruminant lineage after it diverged from the other species; and insertions H and I occurred after divergence of the cetacean lineage.

That's just a quick layman-level overview of *one* of the many ways that whale evolution has been verified. For more technical examinations along several independent lines of evidence, see for example:
SINE Evolution, Missing Data, and the Origin of Whales

Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales

Evidence from Milk Casein Genes that Cetaceans are Close Relatives of Hippopotamid Artiodactyls

Analyses of mitochondrial genomes strongly support a hippopotamus±whale clade

A new, diminutive Eocene whale from Kachchh (Gujarat, India) and its implications for locomotor evolution of cetaceans

A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales

Mysticete (Baleen Whale) Relationships Based upon the Sequence of the Common Cetacean DNA Satellite1

The Mitochondrial Genome of the Sperm Whale and a New Molecular Reference for Estimating Eutherian Divergence Dates

Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss

Eocene evolution of whale hearing

Novel Phylogeny of Whales Revisited but Not Revised

Land-to-sea transition in early whales: evolution of Eocene Archaeoceti (Cetacea) in relation to skeletal proportions and locomotion of living semiaquatic mammals

Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes

New Morphological Evidence for the Phylogeny of Artiodactyla, Cetacea, and Mesonychidae

Cetacean Systematics


Phylogenetic Relationships of Artiodactyls and Cetaceans as Deduced from the Comparison of Cytochrome b and 12s rRNA Mitochondrial Sequences

Molecular evolution of mammalian ribonucleases

And much, much more.

Evolution of army ants

I got curious about the actual study, so after reading the Cornell press release, I went and bought a copy of the actual study from PNAS Online ("Evolution of the army ant syndrome: The origin and long-term evolutionary stasis of a complex of behavioral and reproductive adaptations").

The first thing I found is that there's a reason why creationists really ought to break their habit of learning their "science" from a) creationist sites or b) press releases (and why evolutionists more often than not read the primary literature, which is something I've almost never seen a creationist doing).

The press release did indeed say that "because since the reign of the dinosaurs, about 100 million years ago, army ants in essence have not changed a bit". But this is just the reporter's piss-poor misunderstanding (and therefore misrepresentation) of what the study *actually* determined. Nowhere in the study itself is there any hint of a claim that army ants "haven't changed a bit" in the past 100 million years.

What it *does* say is:

The army ant syndrome of behavioral and reproductive traits (obligate collective foraging, nomadism, and highly specialized queens) has allowed these organisms to become the premiere social hunters of the tropics [...] Results strongly indicate that the suite of behavioral and reproductive adaptations found in army ants throughout the world is inherited from a unique common ancestor [...] Because no known army ant species lacks any component of the army ant syndrome, this group represents an extraordinary case of long-term evolutionary stasis in these adaptations.
In other words, the three *characteristics* which make an army ant what it is (1. foraging in groups -- most non-army ants use scouts, 2. nomadic lifestyle -- most non-army ants nest in one place, 3. flightless queens which can pump out *millions* of eggs) came into being 100 million years ago and have persisted ever since. Needless to say, that's quite a different thing than the much more general "army ants haven't changed a bit" claim the reporter made.

Nor is the press release's headline accurate or supported by the study ("Army ants, as voracious as ever, have defied evolution for 100 million years, Cornell entomologist finds ").

There's nothing in the study about "defying evolution". The only thing I could find which the reporter might have (very badly) mistaken for such a claim is where the author points out that previous *assumptions* (which were recognized to be no more than assumptions) were that "old world" and "new world" army ants may have evolved separately from non-army ancestors on their respective continents. Instead, this study finds, there was a single army-ant ancestor and all modern army ant families/species descended from them. So the results of this study "defy" previous presumptions about how army ants may have evolved, but hardly "defy" evolution itself.

Someone shoot that reporter...

Meanwhile, the study's findings are interesting in their own right, and add yet more data to the massive mountains of hard evidence *for* evolution (which insulting cartoons by our resident creationists do nothing to refute).

Using a variety of measures (DNA base-pair sequences consisting of three nuclear and one mitochondrial gene totalling 3538 basepairs from each of the 49 extant ant species, fossil evidence, and 116 morphological metrics), the author's mathematical analysis produced a cladistic tree for both army ants and many non-army ant species as follows:

The letters (A-H) indicate points in time where the subsequent "branches" are known to have already existed, because representatives from each "branch" have been disocovered in the fossil record.

The branches marked with "*" are branches where the ML tree analysis produced results with "a posterior probability of >95% after independent Bayesian phylogenetic analysis".

As described in the press release, this does indeed clearly indicate that all modern army ants (species shown in bold type) descended from a common ancestor, instead of from two or more common ancestors which were themselves not army ants.

It's also interesting to note that all the "old world" (OW) and "new world" (NW) army ants are separate branches of the oldest split of the army ant family tree. This demonstrates that, as previously presumed, the lifestyle of the army ant (especially, wingless queens) precludes any cross-continental "crossovers", where some species had (during the last 100 million years) managed to travel from one continent to another and take up new residence there.

This correct presumption -- along with the incorrect presumption that army ants had appeared more recently than 100 million years ago -- was the basis for the original assumption that old-world and new-world army ants had perhaps evolved independently (on their respective continents).

Instead, this DNA and morphological analysis (which, by the way, does *not* depend on a "genetic clock") strongly indicates that army ants first arose approximately 105 million years ago.

The reason that this is such an interesting result is that it *very* closely matches the known time of existence of the Cretaceous super-continent of Gondwana, *and* the time of the old-world/new-world army ant split matches the known time of the break-up of that supercontinent into separate continents which contain what is now South America (on one side) and Africa (on the other), the respective homes of the new-world and old-world army ants.

In other words, the analysis strongly matches an evolutionary model in many different ways, including several I haven't even mentioned here.

First, the fact that such a "family tree" works out *at all* is strong evidence that evolution has actually taken place. If instead ants of various species and/or "kinds" had been separately created, there's no reason at all that their DNA details *and* their fossil traces *and* their morphological details would so neatly fit a timewise evolutionary tree of common descent *at all*. For just one example, if the species at the top of the tree and the bottom of the tree shared a characteristic gene sequence, while the other species didn't (because, say, God felt they each would benefit from it), then the entire tree structure would be blatantly violated. Instead, every time DNA/morphological data is analyzed in this way, even across widely divergent species like cows and giraffes and whales, an implied "tree of common descent" is inarguably implied by the evidence.

Second, in this case, the "family tree" implied by the evidence "just happens" to *exactly* match geologic events which would be expected to explain parts of the tree if it came about via evolution. For example, if all modern army ants had a common ancestor, then at some point in time the ancestral army ant must have arisen at a particular geographic location (obviously). This would be a problem if, for example, the data implied that this happened at a time before ants existed at all, or after army ants were known to exist in fossils, etc. And yet, when the available evidence is objectively analyzed by a mathematical algorithm with no ideological ax to grind, the results beautifully match an evolutionary origin consistent with the known fossil record, timewise.

Furthermore, red flags would be raised if the time-and-place of the calculated origin happened to fall in a place where army ants would be highly unlikely to have gotten from their point of origin to the separate continents where they are seen today (e.g. South America and Africa). But lo and behold, the analysis shows the time-and-place of the calculated origin to be at a time when those two continents were known to be joined.

Furthermore, the calculated split between old-world and new-world army ants is found to fall at a time when the continents themselves split apart, perfectly explaining how and why the populations on each new continent, now isolated, should (and thus did) diverge into families of species which evolved in unrelated directions from each other (thus forming species that, while all still army ants in lifestyle, show characteristic differences).

And so on and so on.

Again and again, every time studies and analyses like this -- and every other conceivable type -- are performed, the results "just happen" to fall in a way that makes perfect sense if modern (and fossil) life had arisen from earlier life forms in a common-descent, evolutionary process, like individual jigsaw puzzle pieces all of which form a smooth, coherent picture (albeit with some pieces still not yet discovered) where all the pieces found so far all mesh smoothly with their neighbors.

If evolution is *not* true, why does the jigsaw puzzle formed by the mountains of evidence so well match the evolutionary picture predicted by the theory?

Evolution of the vertebrate clotting mechanism

In detail, discuss why gradual evolution of blood clotting with 10 protein feedback loops all working at once is actually quite feasible evolutionarily speaking.

Well, okay, since you insist... Check out The Evolution of Vertebrate Blood Clotting, or The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes. Excerpt from the latter paper:

It is thought that 50–100 million years separate the appearances of urochordates (which include the sea squirt) and vertebrates. During that time the machinery for thrombin-catalyzed fibrin formation had to be concocted by gene duplication and the shuffling about of key modular domains. The relative times of duplicative events can be estimated by various means, the most obvious being the presence or absence of a gene in earlier diverging organisms, although it must be kept in mind that lineages may lose genes. Another way to gauge events is from the relative positions of various gene products on phylogenetic trees, earlier branching implying earlier appearance. In this regard, (pro)thrombin invariably appears lower on the phylogenetic trees than do the other vitamin K-dependent factors (Fig. 2).

The order of events can also be inferred by considering the most parsimonious route to assembling the various clusters of peripheral domains. Nine of the proteases under discussion can be accounted for by six domain-swapping events (Fig. 5). Indeed, the presence of a multiple-kringle protease in the sea squirt genome provides a reasonable model for a step-by-step parallel evolution of the clotting and lysis systems. It should be noted that a serine protease with only one kringle has been found in the ascidian Herdmania momus (36). Although numerous scenarios have been offered in the past about how modular exchange was involved in generating these schemes (refs. 4, 12, and 37–41, inter alia), the new genomic data now provide a realistic set of starting materials.

Also, Evolution of enzyme cascades from embryonic development to blood coagulation:
Recent delineation of the serine protease cascade controlling dorsal-ventral patterning during Drosophila embryogenesis allows this cascade to be compared with those controlling clotting and complement in vertebrates and invertebrates. The identification of discrete markers of serine protease evolution has made it possible to reconstruct the probable chronology of enzyme evolution and to gain new insights into functional linkages among the cascades. Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks.
That was the abstract. An excerpt from the text:
The downstream protease of the vertebrate clotting cascade (Fig. 1d), thrombin, belongs to the same lineage as complement factors C1r and C1s. The upstream and middle proteases of the clotting cascade (factors VII, IX and X) belong to the most modern lineage, that of horseshoe crab clotting factor C. Therefore, the lineage of thrombin is parental to that of the upstream and middle proteases of the clotting cascade (Table 1) and distinguishes it from the other vitamin-K-dependent clotting proteases (factors VII, IX and X, and protein C). This conclusion agrees with sequence and species comparisons implying that thrombin was the ancestral blood-clotting protein [11]. It also suggests that vertebrate blood clotting emerged as a by-product of innate immunity, because the entire functional core of vertebrate clotting shares ancestry with complement proteases.
And if that's not enough, you could check these out:
Banyai, L., Varadi, A. and Patthy, L. (1983). “Common evolutionary origin of the fibrin-binding structures of fibronectin and tissue-type plasminogen activator.” FEBS Letters, 163(1): 37-41.

Bazan, J. F. (1990). “Structural design and molecular evolution of a cytokine receptor superfamily.” Proceedings of the National Academy of Sciences of the United States of America, 87(18): 6934-6938.

Blake, C. C. F., Harlos, K. and Holland, S. K. (1987). “Exon and Domain Evolution in the Proenzymes of Blood Coagulation and Fibrinolysis.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 925-932.

Fornace AJ Jr, Cummings DE, Comeau CM, Kant JA, Crabtree GR. “The Structure of the human gamma-fibrinogen gene. Alternate mRNA splicing near the 3' end of the gene produces gamma A and gamma B forms of gamma-fibrinogen.” J Biol Chem. 1984 Oct 25;259(20):12826-30.

Crabtree, G. R., Comeau, C. M., Fowlkes, D. M., Fornace, A. J., Jr., Malley, J. D. and Kant, J. A. (1985). “Evolution and structure of the fibrinogen genes: Random insertion of introns or selective loss?” Journal of Molecular Biology, 185(1): 1-20.  

Di Cera, E., Dang, Q. D. and Ayala, Y. M. (1997). “Molecular mechanisms of thrombin function.” Cell Mol Life Sci, 53(9): 701-730.  

Doolittle, R. F. (1985). “More homologies among the vertebrate plasma proteins.” Biosci Rep, 5(10-11): 877-884.

Doolittle, R. F. (1990). “The Structure and Evolution of Vertebrate Fibrinogen A Comparison of the Lamprey and Mammalian Proteins,” in ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY: FIBRINOGEN, THROMBOSIS, COAGULATION, AND FIBRINOLYSIS. C. Y. Liu and Chien, S. New York, Plenum Press. 281.

Doolittle, R. F. (1992). “A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives.” Protein Science, 1(12): 1563-1577.

Doolittle, R. F. (1992). “Early Evolution of the Vertebrate Fibrinogen Molecule.” Biophysical Journal, 61(2 PART 2): A410.  

Doolittle, R. F. (1992). “Stein and Moore Award address. Reconstructing history with amino acid sequences.” Protein Science, 1(2): 191-200.

Doolittle, R. F. (1993). “The Evolution of Vertebrate Blood Coagulation - a Case of Yin and Yang.” Thrombosis and Haemostasis, V70(N1): 24-28.

Doolittle, R. F. and Feng, D. F. (1987). “Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins.” Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 869-874.

Doolittle, R. F., G., Spraggon and J., Everse S. (1997). “Evolution of vertebrate fibrin formation and the process of its dissolution.” Ciba Found Symp, 212: 4-17; discussion 17-23.

Doolittle, R. F. and Riley, M. (1990). “The amino-terminal sequence of lobster fibrinogen reveals common ancestry with vitellogenins.” Biochemical and Biophysical Research Communications, 167(1): 16-19.

Edgington, T. S., Curtiss, L. K. and Plow, E. F. (1985). “A linkage between the hemostatic and immune systems embodied in the fibrinolytic release of lymphocyte suppressive peptides.” Journal of Immunology, 134(1): 471-477.  

Ghidalia, W., Vendrely, R., Montmory, C., Coirault, Y., Samama, M., Lucet, B., Bellay, A. M. and Vergoz, D. (1989). “Overall study of the in vitro plasma clotting system in an invertebrate, Liocarcinus puber (Crustacea Decapoda): Considerations on the structure of the Crustacea plasma fibrinogen in relation to evolution.” Journal of Invertebrate Pathology, 53(2): 197-205.  

Hervio, L. S., Coombs, G. S., Bergstrom, R. C., Trivedi, K., Corey, D. R. and Madison, E. L. (2000). “Negative selectivity and the evolution of protease cascades: the specificity of plasmin for peptide and protein substrates.” Chemistry & Biology, V7(N6): 443-452.  

Hewett-Emmett, D., Czelusniak, J. and Goodman, M. (1981). “The evolutionary relationship of the enzymes involved in blood coagulation and hemostasis.” Annals of the New York Academy of Sciences, 370(20): 511-527.  

Holland, S. K., Harlos, K. and Blake, C. C. F. (1987). “Deriving the generic structure of the fibronectin type II domain from the prothrombin Kringle 1 crystal structure.” EMBO (European Molecular Biology Organization) Journal, 6(7): 1875-1880.  

Jordan, R. E. (1983). “Antithrombin in vertebrate species: conservation of the heparin-dependent anticoagulant mechanism.” Archives of Biochemistry and Biophysics, 227(2): 587-595.  

Kant, J. A., Fornace, A. J., Jr., Saxe, D., Simon, M. J., McBride, O. W. and Crabtree, G. R. (1985). “Evolution and organization of the fibrinogen locus on chromosome 4: Gene duplication accompanied by transposition and inversion.” Proceedings of the National Academy of Sciences of the United States of America, 82(8): 2344-2348.  

Kornblihtt, A. R., Pesce, C. G., Alonso, C. R., Cramer, P., Srebrow, A., Werbajh, S. and Muro, A. F. (1996). “The fibronectin gene as a model for splicing and transcription studies.” FASEB Journal, 10(2): 248-257.  

Laki, K. (1972). “Our ancient heritage in blood clotting and some of its consequences.” Annals of the New York Academy of Sciences, 202(4): 297-307.  

Neurath, H. (1984). “Evolution of proteolytic enzymes.” Science, 224(4647): 350-357.

Neurath, H. (1986). “The Versatility of Proteolytic Enzymes.” Journal of Cellular Biochemistry, 32(1): 35-50.  

Oldberg, A. and Ruoslahti, E. (1986). “Evolution of the fibronectin gene: Exon structure of cell attachment domain.” Journal of Biological Chemistry, 261(5): 2113-2116.  

Opal, S. M. (2000). “Phylogenetic and functional relationships between coagulation and the innate immune response.” Critical Care Medicine, V28(N9 SUPPS): S77-S80.  

Pan, Y. and Doolittle, R. F. (1991). “Distribution of Introns in Lamprey Fibrinogen Genes.” Journal of Cellular Biochemistry Supplement(15 PART D): 75.  

Pan, Y. and Doolittle, R. F. (1992). “cDNA sequence of a second fibrinogen alpha chain in lamprey: an archetypal version alignable with full-length beta and gamma chains.” Proceedings of the National Academy of Sciences of the United States of America, 89(6): 2066-2070.

Patthy, L. (1985). “Evolution of the Proteases of Blood Coagulation and Fibrinolysis by Assembly from Modules.” Cell, 41(3): 657-664.

Patthy, L. (1990). “Evolution of blood coagulation and fibrinolysis.” Blood Coagulation and Fibrinolysis, 1(2): 153-166.

Patthy, L. (1990). “Evolutionary Assembly of Blood Coagulation Proteins.” Seminars in Thrombosis and Hemostasis, 16(3): 245-259.

Patthy, L. (1999). “Genome evolution and the evolution of exon-shuffling—a review.” Gene, 238(1): 103-114.

Roberts, Lewis R., Nichols, Lanita A. and Holland, Lene J. (1995). “CDNA and amino-acid sequences and organization of the gene encoding the B-beta subunit of fibrinogen from Xenopus laevis.” Gene (Amsterdam), 160(2): 223-228.  

Sosnoski, D. M., Emanuel, B. S., Hawkins, A. L., Van Tuinen, P., Ledbetter, D. H., Nussbaum, R. L., Kaos, F. T., Schwartz, E., Phillips, D. and et al. (1988). “Chromosomal localization of the genes for the vitronectin and fibronectin receptors .alpha. subunits and for platelet glycoproteins IIb and IIIa.” Journal of Clinical Investigation, 81(6): 1993-1998.  

Wang, Y. Z., Patterson, J., Gray, J. E., Yu, C., Cottrell, B. A., Shimizu, A., Graham, D., Riley, M. and Doolittle, R. F. (1989). “Complete sequence of the lamprey fibrinogen .alpha. chain.” Biochemistry, 28(25): 9801-9806.  

Xu, X. and Doolittle, R. F. (1990). “Presence of a vertebrate fibrinogen-like sequence in an echinoderm.” Proceedings of the National Academy of Sciences of the United States of America, 87(6): 2097-2101.

Zhang, Y. L., Hervio, L., Strandberg, L. and Madison, E. L. (1999). “Distinct contributions of residue 192 to the specificity of coagulation and fibrinolytic serine proteases.” Journal of Biological Chemistry, V274(N11): 7153-7156.

Zimmermann, E. (1983). “[The evolution of the coagulation system from primitive defense mechanisms].” Behring Institute Mitteilungen, 82(73): 1-12.  

The 2.0-Å crystal structure of tachylectin 5A provides evidence for the common origin of the innate immunity and the blood coagulation systems

Davidson CJ, Tuddenham EG, McVey JH. 450 million years of hemostasis J Thromb Haemost. 2003 Jul;1(7):1487-94.

And so on...

Evolution of the Krebs metabolic cycle:

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

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

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

The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution, Melendez-Hevia E, Waddell TG, Cascante M, J Mol Evol. 1996 Sep;43(3):293-303
A portion of the abstract:
Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
From the body of the article:
In the evolution of the metabolism, the achievement of the fundamental steps of the Krebs cycle was not difficult at all. Almost all of its structure previously existed for very different purposes (anabolic), and cells had to add just one enzyme (succinyl-CoA synthetase for the transformation of succynol CoA into succinate) to convert a collection of different pathways into the central cyclic pathway of the metabolism. This is one of the most clear cases of opportunism we can find in evolution.


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

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

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

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

The Molecular Anatomy of an Ancient Adaptive Event: Protein engineering identifies the structural basis of a 3.5 billion-year-old adaptation, Antony Dean, American Scientist, Volume: 86 Number: 1 Page: 26 DOI: 10.1511/1998.1.26
In short, the Krebs cycle arose as a relatively minor modification to pre-existing cellular biochemical processes which were being used for amino acid synthesis and early iron-based metabolism.

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

The universal ancestor was a thermophile or a hyperthermophile: tests and further evidence, Di Giulio M., J Theor Biol. 2003 Apr 7;221(3):425-36
...which is only one of the recent confirmations of this model of the origin of life as we know it:
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells, William Martin and Michael J. Russell, Phil. Trans. R. Soc. Lond. B, DOI 10.1098/rstb.2002.1183
A related observation is:
"The oldest of these proteins was ferredoxin, a biosynthesis enzyme that contains iron-sulfur clusters and that transfers electrons (hydrogen-atom equivalents). This protein he reconstructs as having a negatively-charged tail; this can stick to positively-charged objects like mineral surfaces with their metal ions -- which is consistent with the view of Gunter Wachtershauser that life originated from iron-sulfur-associated chemical reactions on mineral surfaces, and that the Krebs Cycle dates from this time. Note that the Krebs Cycle's members are all acids -- negatively-charged ions -- meaning that they can stick to mineral surfaces."
-- from this webforum discussion
In short, life most likely originated in iron monosulphide pockets around hydrothermal ocean vents.


(Note, a recent change at NCBI has broken a lot of these links, but you can still find those papers by Googling for their titles):

The Evolution of Improved Fitness by random mutation plus selection

Ancient Jumping DNA May Have Evolved Into Key Component Of Human Immune System

Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system

Evolution of immune reactions

New insights into V(D)J recombination and its role in the evolution of the immune system

Evolution and developmental regulation of the major histocompatibility complex

Evolution of the IL-6/class IB cytokine receptor family in the immune and nervous systems

Layered evolution in the immune system. A model for the ontogeny and development of multiple lymphocyte lineages

Development of an immune system

The ancestor of the adaptive immune system was the CAM system for organogenesis

The evolutionary origins of immunoglobulins and T-cell receptors: possibilities and probabilities

Evolutionary perspectives on amyloid and inflammatory features of Alzheimer disease

Organization of the human RH50A gene (RHAG) and evolution of base composition of the RH gene family.

Molecular evolution of the vertebrate immune system.

Morphostasis: an evolving perspective.

Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells.

Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins

Evolutionary assembly of blood coagulation proteins

Exon and domain evolution in the proenzymes of blood coagulation and fibrinolysis

Evolution of proteolytic enzymes

Evolution of vertebrate fibrin formation and the process of its dissolution.

Common Parasite Overturns Traditional Beliefs About The Evolution And Role Of Hemoglobin

Scientists Discover How Bacteria Protect Themselves Against Immune System

The Evolution of Hemoglobin

Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships

Reduction of two functional gamma-globin genes to one: an evolutionary trend in New World monkeys

Evolutionary history of introns in a multidomain globin gene

Hemoglobin A2: origin, evolution, and aftermath

Early evolution of microtubules and undulipodia

Flagellar beat patterns and their possible evolution

A temporary flagellate (mastigote) stage in the vahlkampfiid amoeba Willaertia magna and its possible evolutionary significance

The evolutionary origin and phylogeny of eukaryote flagella

Molecular analysis of archael flagellins: similarity to the type IV pilin-transport superfamily widespread in bacteria

Molecular evolution of the C-terminal cytoplasmic domain of a superfamily of bacterial receptors involved in taxis

Dynein family of motor proteins: present status and future questions

Origins of the nucleate organisms

The evolutionary origin and phylogeny of microtubules, mitotic spindles and eukaryote flagella

The evolution of cellular movement in eukaryotes: the role of microfilaments and microtubules

Kinesin Motor Phylogenetic Tree

Evolution of a dynamic cytoskeleton

Isolation, characterization and evolution of nine pufferfish (Fugu rubripes) actin genes

Evolution of chordate actin genes: evidence from genomic organization and amino acid sequences

Structural comparisons of muscle and nonmuscle actins give insights into the evolution of their functional differences

Molecular evolution of glutamate receptors: a primitive signaling mechanism that existed before plants and animals diverged.

Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides

The evolution of the synapses in the vertebrate central nervous system

Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria.

A comprehensive evolutionary analysis based on nucleotide and amino acid sequences of the alpha- and beta-subunits of glycoprotein hormone gene family.

The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution

The evolution of metabolic cycles

Evolution of the first metabolic cycles

Chemical evolution of the citric acid cycle: sunlight photolysis of the amino acids glutamate and aspartate

Speculations on the origin and evolution of metabolism

The Molecular Anatomy of an Ancient Adaptive Event

New prospects for deducing the evolutionary history of metabolic pathways in prokaryotes: aromatic biosynthesis as a case-in-point

Biochemical pathways in prokaryotes can be traced backward through evolutionary time

Enzyme specialization during the evolution of amino acid biosynthetic pathways

Enzyme recruitment in evolution of new function

Evolution of glycolysis

Bioenergetics: the evolution of molecular mechanisms and the development of bioenergetic concepts

Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis

The evolution of kinetoplastid glycosomes

Stepwise molecular evolution of bacterial photosynthetic energy conversion

Evolution of photosynthetic reaction centers and light harvesting chlorophyll proteins

Evolution of photosynthetic reaction centers

Early evolution of photosynthesis: clues from nitrogenase and chlorophyll iron proteins

Evolution of the control of pigment and plastid development in photosynthetic organisms

Chemical evolution of photosynthesis

Molecular evolution of ruminant lysozymes

Adaptive evolution of lysozyme: changes in amino acid sequence, regulation
of expression and gene number

Evolution of stomach lysozyme: the pig lysozyme gene

The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates

The Evolution of Color Vision

Molecular basis for tetrachromatic color vision

Molecular evolution of the Rh3 gene in Drosophila

Interphotoreceptor retinoid-binding protein. Gene characterization, protein repeat structure, and its evolution

Spectral tuning and molecular evolution of rod visual pigments in the species flock of cottoid fish in Lake Baikal

The evolution of rhodopsins and neurotransmitter receptors

Optimization, constraint, and history in the evolution of eyes

A pessimistic estimate of the time required for an eye to evolve

Sequence analysis of teleost retina-specific lactate dehydrogenase C: evolutionary implications for the vertebrate lactate dehydrogenase gene family

The eye of the blind mole rat (Spalax ehrenbergi): regressive evolution at the molecular level

The evolution of eyes.

Programming the Drosophila embryo

Evolution of chordate hox gene clusters

Hox genes in brachiopods and priapulids and protostome evolution.

Radical evolutionary change possible in a few generations

Evolution Re-Sculpted Animal Limbs By Genetic Switches Once Thought Too Drastic For Survival

Flatworms Are Oldest Living Ancestors To Those Of Us With Right And Left Sides Researchers Report In Science

The origin and evolution of animal appendages

Hox genes in evolution: protein surfaces and paralog groups

Evolution of the insect body plan as revealed by the Sex combs reduced expression pattern

Sea urchin Hox genes: insights into the ancestral Hox cluster

Theoretical approaches to the analysis of homeobox gene evolution

Teleost HoxD and HoxA genes: comparison with tetrapods and functional evolution of the HOXD complex

Evolutionary origin of insect wings from ancestral gills

Tracing backbone evolution through a tunicate's lost tail

Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes

Modification of expression and cis-regulation of Hoxc8 in the evolution of diverged axial morphology.

The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster.

Gene duplications in evolution of archaeal family B DNA polymerases

Adaptive amino acid replacements accompanied by domain fusion in reverse transcriptase

Molecular evolution of genes encoding ribonucleases in ruminant species

Studies on the sites expressing evolutionary changes in the structure of eukaryotic 5S ribosomal RNA

Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon

Archaeal translation initiation revisited: the initiation factor 2 and eukaryotic initiation factor 2B alpha-beta-delta subunit families

Universally conserved translation initiation factors

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant

Evolution of transcriptional regulatory elements within the promoter of a mammalian gene.

Codon reassignment and amino acid composition in hemichordate mitochondria.

Reconstructing the evolution of vertebrate blood coagulation from a consideration of the amino acid sequences of clotting proteins

Determining divergence times of the major kingdoms of living organisms with a protein clock

The multiplicity of domains in proteins

Characterization, primary structure, and evolution of lamprey plasma albumin

The origins and evolution of eukaryotic proteins

Evolution of vertebrate fibrin formation and the process of its dissolution.

Vastly Different Virus Families May Be Related

Selective sweep of a newly evolved sperm-specific gene in Drosophila

Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions

Molecular evolution of the histidine biosynthetic pathway

Accelerated evolution in inhibitor domains of porcine elafin family members

Tandem arrangement of the human serum albumin multigene family in the sub-centromeric region of 4q: evolution and chromosomal direction of transcription

The B12-dependent ribonucleotide reductase from the archaebacterium Thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum

Ancient divergence of long and short isoforms of adenylate kinase: molecular evolution of the nucleoside monophosphate kinase family

Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod

Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish

Evolution of an antifreeze glycoprotein

A model for the evolution of the plastid sec apparatus inferred from secY gene phylogeny

The evolutionary history of the amylase multigene family in Drosophila pseudoobscura

Accelerated evolution of Trimeresurus okinavensis venom gland phospholipase A2 isozyme-encoding genes

The evolution of an allosteric site in phosphorylase

Molecular evolution of fish neurohypophysial hormones: neutral and selective evolutionary mechanisms

Pseudogenes in ribonuclease evolution: a source of new biomacromolecular function?

Evolution of hemopoietic ligands and their receptors. Influence of positive selection on correlated replacements throughout ligand and receptor proteins

Evolutionary relationships of the carbamoylphosphate synthetase genes

The molecular evolution of the small heat-shock proteins in plants

Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life

Duplication and functional divergence in the chalcone synthase gene family of Asteraceae: evolution with substrate change and catalytic simplification

Evolutionary history of the 11p15 human mucin gene family.

Molecular evolution of the aldo-keto reductase gene superfamily.

Molecular evolution allows bypass of the requirement for activation loop phosphorylation of the Cdc28 cyclin-dependent kinase.

A Classification of Possible Routes of Darwinian Evolution

Generation of evolutionary novelty by functional shift

Mobile DNA Sequences Could Be The Cause Of Chromosomal Mutations During The Evolution Of Species

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution.

The domain model for eukaryotic DNA organization. 2: A molecular basis for constraints on development and evolution.

Minor Shuffle Makes Protein Fold

Genetic Stowaways May Contribute To Evolutionary Change

Evolutionary Molecular Mechanism In Mammals Found

Complete Genomes

Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators

Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families

Cases of ancient mobile element DNA insertions that now affect gene regulation

Punctuated evolution caused by selection of rare beneficial mutations

The origin of programmed cell death

The origin and early development of biological catalysts

DNA secondary structures and the evolution of hypervariable tandem arrays

Episodic adaptive evolution of primate lysozymes

Genome plasticity as a paradigm of eubacteria evolution

Evolutionary motif and its biological and structural significance

Neutral and nonneutral mutations: the creative mix--evolution of complexity in gene interaction systems

Exon shuffling and other ways of module exchange

Introns and gene evolution

New Drosophila introns originate by duplication.

Evolution and the structural domains of proteins

The role of constrained self-organization in genome structural evolution

A possible origin of newly-born bacterial genes: significance of GC-rich nonstop frame on antisense strand

The coevolution of gene family trees

The evolution of metabolic cycles

The emergence of major cellular processes in evolution

A hardware interpretation of the evolution of the genetic code

Speculations on the origin and evolution of metabolism

Probabilistic reconstruction of ancestral protein sequences

The contribution of slippage-like processes to genome evolution

Molecular evolution in bacteria

The structural basis of molecular adaptation.

Mitochondrial DNA: molecular fossils in the nucleus

Cases of ancient mobile element DNA insertions that now affect gene regulation

Tiggers and DNA transposon fossils in the human genome

The eye of the blind mole rat (Spalax ehrenbergi): regressive evolution at the molecular level

Tiggers and DNA transposon fossils in the human genome

Gene competition and the possible evolutionary role of tumours

New Scientist Planet Science: Replaying life

Molecular evolution of an arsenate detoxification pathway by DNA shuffling

UB Researcher Developing Method That Employs Evolution To Develop New Drug Leads

Directed evolution of a type I antifreeze protein expressed in Escherichia coli with sodium chloride as selective pressure and its effect on antifreeze tolerance

Directed evolution of biosynthetic pathways. Recruitment of cysteine thioethers for constructing the cell wall of Escherichia coli

Exploring the functional robustness of an enzyme by in vitro evolution

Evolutionary algorithms in computer-aided molecular design

Mutations to the Rescue

Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment

Evolution of Amino Acid Metabolism Inferred through Cladistic Analysis

Integrating the Universal Metabolism into a Phylogenetic Analysis

Invertebrate Data Predict an Early Emergence of Vertebrate Fibrillar Collagen Clades and an Anti-incest Model

Tachykinin and Tachykinin Receptor of an Ascidian, Ciona intestinalis: EVOLUTIONARY ORIGIN OF THE VERTEBRATE TACHYKININ FAMILY

DNA Replication Fidelity

Serial segmental duplications during primate evolution result in complex human genome architecture

Phylogeny determined by protein domain content

Evolutionary Genomics of Nuclear Receptors: From Twenty-Five Ancestral Genes to Derived Endocrine Systems

Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution

The Evolution of Controlled Multitasked Gene Networks: The Role of Introns and Other Noncoding RNAs in the Development of Complex Organisms

Phylogenetic Dating and Characterization of Gene Duplications in Vertebrates: The Cartilaginous Fish Reference

Dating the Tree of Life

An Insect Molecular Clock Dates the Origin of the Insects and Accords with Palaeontological and Biogeographic Landmarks

Diversity, taxonomy and evolution of medium-chain dehydrogenase/reductase superfamily

Molecular archaeology of the Escherichia coli genome

Comparative Genomics of the Eukaryotes

Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome

Asymmetric Sequence Divergence of Duplicate Genes

The Genetic Core of the Universal Ancestor

Evolutionary History of Chromosome 20

The Complete Mitochondrial DNA Sequence of Scenedesmus obliquus Reflects an Intermediate Stage in the Evolution of the Green Algal Mitochondrial Genome

Reconstructing large regions of an ancestral mammalian genome in silico

Occurrence and Consequences of Coding Sequence Insertions and Deletions in Mammalian Genomes

The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals

Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles

Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea

The Evolution of Trichromatic Color Vision by Opsin Gene Duplication in New World and Old World Primates

Obcells as Proto-Organisms: Membrane Heredity, Lithophosphorylation, and the Origins of the Genetic Code, the First Cells, and Photosynthesis (Journal of Molecular Evolution, Volume 53 - Number 4/5, 2001)

N-Carbamoyl Amino Acid Solid-Gas Nitrosation by NO/NOx: A New Route to Oligopeptides via alpha-Amino Acid N-Carboxyanhydride. Prebiotic Implications (Journal of Molecular Evolution, Volume 48 - Number 6, 1999

Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code (Naturwissenschaften, Volume 89 Number 12 December 2002)

The Nicotinamide Biosynthetic Pathway Is a By-Product of the RNA World (Journal of Molecular Evolution, Volume 52 - Number 1, 2001)

On the RNA World: Evidence in Favor of an Early Ribonucleopeptide World

Inhibition of Ribozymes by Deoxyribonucleotides and the Origin of DNA

How much more evidence would you like to see?
104 posted on 04/12/2005 9:29:46 PM PDT by Ichneumon
[ Post Reply | Private Reply | To 81 | View Replies]

To: Ichneumon

105 posted on 04/12/2005 9:48:38 PM PDT by RightWingAtheist (Creationism is not conservative!)
[ Post Reply | Private Reply | To 104 | View Replies]

To: qam1
According to the Hebrew dictionary, the verses you gave in your post are not translated as accurately as they are in the old KJV.

Gen 1:20 And God said, Let the waters swarm with swarms of living creatures, and let birds fly above the earth, and in the open firmament of heaven.

Gen 1:21 And God created the great sea monsters, and every living creature that moveth, wherewith the waters swarmed, after their kind, and every winged bird after it's kind; and God saw that it was good.

Gen 2:19 And out of the ground Jehovah God formed every beast of the field, and every bird of the heavens.............

Gen 1:20-21 as written in Hebrew does not say that God created birds out of the water. The terms "brought forth" in your 1:20 quotation and "bring forth" in your 1:21 quote are all translations of the one Hebrew word sharats, which means wriggle, or swarm, or by implication, abound. Therefore in the language of Moses, the verse would read something like, "And let the waters swarm or wriggle or abound with the moving creature that hath life, and with fowl that may fly.......IOW, the term used in the KJV. To "let the waters sharats (swarm) with the creature that moveth and with fowl that may fly" does not necessarily mean that those creatures and fowl were formed from those waters.

In the language spoken by Moses Gen 2:19 says that out of adamah every beast of the field, and every fowl that flies was formed. adamah translates to earth or soil or ground. Is it not true that all animal tissue, bird tissue included, is composed of some elements of the earth?

Even if you translate sharats as "bring forth", as it reads in your translation, there is no real conflict between the accounts in chapters 1 and 2, unless of course one chooses to see a conflict that supports his or her argument.

106 posted on 04/12/2005 11:19:24 PM PDT by epow (Bibles that are falling apart usually belong to people who aren't.)
[ Post Reply | Private Reply | To 103 | View Replies]

To: Ichneumon
#104; Ichy you go on, and on , and on; like that..
If somebody b!tch slapped the Pope of Evolution..
I want to know which post was that.?.
Somebody must've performed some sacrilage of some sort..
107 posted on 04/12/2005 11:19:33 PM PDT by hosepipe (This Propaganda has been edited to include not a small amount of Hyperbole..)
[ Post Reply | Private Reply | To 104 | View Replies]

To: 3dognight

For some, evolution is a religion.

108 posted on 04/12/2005 11:21:17 PM PDT by k2blader (Immorality bites.)
[ Post Reply | Private Reply | To 4 | View Replies]

To: presidio9
eep eep eep, oop, oop, oop
109 posted on 04/12/2005 11:23:03 PM PDT by HiTech RedNeck (No wonder the Southern Baptist Church threw Greer out: Only one god per church! [Ann Coulter])
[ Post Reply | Private Reply | To 1 | View Replies]

To: qam1
The use of the perfective tense in 2:19 does not mean or imply that the beasts were created after man was.

The sequence explicitly stated in 1:1 is plants, animals, man, woman (no simultaneity of man and woman is asserted in this sequence).

The sequence implied in 2:4 is plants, animals, man, woman.

The 2:4 sequence focuses on man, and the narrative at this point only discusses other creatures insofar as they relate directly to man.

Moreover, 1:21 does not imply that fowls came from the water. Another way of translating it, which is more in keeping with the Hebrew, is "God created the great sea monsters and every living creature that moves, with which the waters swarmed after their kind, and every winged bird after its kind; and God saw that it was good."

That's from the NASB translation.

110 posted on 04/13/2005 4:03:12 AM PDT by wideawake (God bless our brave soldiers and their Commander in Chief)
[ Post Reply | Private Reply | To 103 | View Replies]

To: Agamemnon; presidio9
Thank you, Agamemnon.

I also attended a Catholic school and I also was taught fraudulent analysis of the Bible from the viewpoint of what one Catholic scholar rightly calls "the hermeneutic of suspicion".

There are plenty of Catholics as well who reject the documentary hypothesis, the two-source theory, the imaginary Q, etc.

I am a Roman catholic and I do not buy nineteenth-century German Protestant criticism either.

You bring up an important point: Jesus acknowledges the Law as the books of Moses.

He does not describe the Scriptures of the Jews as fables or similes or anything other than the truth of God.

The entire point of Genesis criticism is to turn Adam into a legend instead of the real person he was.

If Adam was not a real person, his sin was merely metaphorical. If his sin was merely metaphorical, then Christ and St. Paul were deceived and the Scriptures are false.

But Adam was a real man, he sinned, and Christ came and really died to redeem us from Adam's sin.

111 posted on 04/13/2005 4:11:41 AM PDT by wideawake (God bless our brave soldiers and their Commander in Chief)
[ Post Reply | Private Reply | To 100 | View Replies]

To: Ichneumon

[Thunderous applause! It continues ... subsides briefly ... then resumes ... louder then before ... it rolls on, and on, and on ...]

112 posted on 04/13/2005 4:18:03 AM PDT by PatrickHenry (<-- Click on my name. The List-O-Links for evolution threads is at my freeper homepage.)
[ Post Reply | Private Reply | To 104 | View Replies]

To: Ichneumon
"And several features of these DNA relics can be used to demonstrate common descent"

Given the size of your post, after this, I didn't read the whole thing.

This statement presupposes that the virus did not cross species. You may say, 'well, even if it did, it couldn't have left the same bits of DNA (e.g. fossils) in the genetic makeup of the other species'. But that question would deny the very essence of chance upon which the theory of evolution is built.

113 posted on 04/13/2005 6:05:44 AM PDT by MEGoody (Ye shall know the truth, and the truth shall make you free.)
[ Post Reply | Private Reply | To 104 | View Replies]

To: narby
I just knew you could spin it.

Again, it has nothing to do with spin. If you can't read carefully it's really not my fault.

If the same author wrote Gen 1:1 and Gen 2:4 as a single story, then they need some medication for schizophrenia.

Wow, that's really insightful analysis. Presumably you're using the "scinetific method" to reach this conclusion? LOL.

The style, tone, as well as specific sequences are different.

The style isn't really different

I really like how you've picked up the word "germinated" from thin air to justify your spin. The KJV uses the term "made ... every plant", and you make up the idea that these plants were ungerminated to carry on your fiction that these aren't two different stories.

The text says "had not yet sprouted" - i.e., germinted. You are quibbling.

Glad you brought up the two stories of Noah as well. More evidence that before the King James Version, and before the oldest existing Hebrew version, there existed earlier versions of Genesis that were merged together from separate sources.

(1) Why would I care about the KJV? I'm a Roman Catholic.

(2) The oldest existing intact Hebrew version of the Scriptures only dates back to the year 1008 AD.

The fact is, you and the critics believe that Hebrews living in the 12th century BC were too primitive and unintelligent to author a rich and complex text.

That's an assumption for which there is no empirical proof - just a bias in the reader.

If you were able to read the Hebrew you would realize that the stylistic differences between Genesis 1 and Genesis 2 are minor and are consistent with any text that moves from a survey/overview to a specific detailed exposition with dialogue. The vocabulary used is the same. The paratactic sentence structure is the same. Even the internal puns are the same.

But I'm sure that's not the version of dogma you were taught, and you'll defend what you were taught until the very end.

I was taught the same nineteenth century kerfuffle you're parroting here.

My first introduction to Scriptural studies was the documentary hypothesis.

I find it fascinating that you claim to be on the side of science and reason, but you proceed by (1) speaking to me condescendingly and insultingly, (2) using obvious logical fallacies like poisoning the well, (3) using hyperbole like "schizophrenia" to describe normal modulation of prose style in a written document.

Bottom line, your version of creation does not belong in a science classroom. It belongs in a seminary.

I don't particularly care whether it ever sees the inside of a classroom. My entire intent in posting was to inform you that facile misrepresentation of the Biblical text is not a winning strategy for you. You can make your argument for your position without denigrating the Scriptures.

114 posted on 04/13/2005 6:30:46 AM PDT by wideawake (God bless our brave soldiers and their Commander in Chief)
[ Post Reply | Private Reply | To 96 | View Replies]

To: Ichneumon

And a cadillac and a Chevy share parts because they were created by design teams with the same pool of parts suppliers and company vision. Some parts seem "irrelevant" to those who do not understand the cars as well as the designer does. It does not mean that "accident" is what introduced them into the design, regardless of how much work one did to come up with their speculative conclusion.

My rebuttal is not as long as your article, but let me give an example of why your whole post could reach a dead end:

In the early 1980's, lived in a suburb of Seattle and worked downtown as a commercial real estate agent. Let's imagine that thousands (or millions) of years from now archeologists dig up some – but not all – of the records of this present day. For arguments sake, lets say they are able to ascertain where I lived, where I worked and things like bus schedules, routes, etc. Let’s further say they were unable to discover my job function at my place of work and only had partial knowledge of our culture and lifestyles.

So, here is what they have discovered about me and my occupation (all true, btw):

I lived less than one block from the bus stop.
My place of business was 1.5 blocks from the downtown bus stop.
My working hours were from 8:30 to 5:30.
The bus left my house at 8:03 and arrived downtown at 8:24.
The bus left downtown at 5:39 and arrived at my house at 6:13.

Their conclusion: I rode the bus to work every day.

It makes sense. And as the old Genesis song says, “They’re trying to find themselves an audience. Their deductions need applause.”

They did a lot of work and came up with some really good analysis. But they are too smart by half, and are dead wrong! I needed my car in my job so I drove to work.

But they didn’t have the information necessary to even guess at that answer. And to make it worse, when I became a computer programmer and, again, worked downtown, I rode my bicycle, leaving the car AND bus.

I don’t mind them saying that they “theorize that Robroy MAY HAVE rode the bus to work," but I don’t want them cramming it down my throat as fact. That is intellectual arrogance, and really makes them look just, well, silly.

And I treat them accordingly.

That said, I have a great deal of respect for those who gather the evidence and say “Robroy MAY HAVE taken the bus, and it is what the evidence we have so far would SUGGEST, but we cannot be certain of what happened. The investigation is ongoing. Once we find the 'missing links' in the data, if we find them, we can then say with certainty how Robroy got to work every day. In the meantime, this is our BEST GUESS.”

And trust me, all hypotheses regarding evolution are "best guesses." Nothing more and nothing less, regardless of how much research, education, "peer reviewed papers" and "facts" with which you care to back it up.

115 posted on 04/13/2005 8:17:18 AM PDT by RobRoy (Child support and maintenence (alimony) are what we used to call indentured slavery)
[ Post Reply | Private Reply | To 104 | View Replies]

To: narby
The Flat Earth society has many very serious members.

They are not dangerous. The scientifically credentialed proponents of Kyoto are; as were the scientifically credentialed proponents of criminal justice reformed based on the theory that criminal behavior is primarily related to one's material envirnoment; as were those claiming that DDT must never be used etc.

116 posted on 04/13/2005 8:26:55 AM PDT by Tribune7
[ Post Reply | Private Reply | To 22 | View Replies]

To: Ichneumon

Absolutely magnificent. Thanks for including me even though I am not on any of the ping lists.

I plan to unabashedly steal your efforts on behalf of a 7 year old grandchild who keeps asking where everything came from. We just finished the evolution of seed plants.

Your organized presentation tops any of my sources and will keep me ahead of the game for at least a little while.

I hope that at least some lurkers will take the time to absorb the information. They are the ones there is some hope of influencing.

117 posted on 04/13/2005 8:50:47 AM PDT by From many - one.
[ Post Reply | Private Reply | To 104 | View Replies]

To: Agamemnon
"Actually, no. Jesus Christ specifically speaks affirmatively of Moses' account of Creation "in the beginning.""

I'm not seeing where it reads that Jesus specifically says that Moses is the author of the stories we see in Genesis. If Moses is the only author, he was quite the confused person indeed, as the accounts, tone, and writing style differ more than you'd expect from a single author.

"I don't particularly care what "higher critics" and pompous-assed "scholars" think about a contrivance known as the JDEP postulate, or what incorrect teaching you happened to receive in a Catholic school. No scholar or nun is greater than Jesus Christ. Do you agree?"

From a Christian perspective, there is no greater scholar than Christ. When Christ comes down from Heaven and tells the world that JDEP is incorrect, then we'll know. Until that time, we're speculating about an event several thousand years ago.

"or do you mistakenly believe that any man, whatever his supposed training or biases, knows more than the Creator of the Universe, Himself?"

There's a difference between not believing what someone says and believing that what they've said isn't what some think. In Catholic school, we looked at the reality of the situation. The words of Jesus were written down by imperfect men years after they were said. The ideas and concepts, we were taught, were preserved by the influence of the Holy Spirit upon the writers.

Now that makes a whole lot more sense to me than anything that says the writers had picture-perfect memories or had their free will and human imperfection suspended for a while by God so they wouldn't get little details a bit off, but that's me.

"I'll even challenge you to produce one archaeolgical find that contradicts a thing that Jesus Christ or Moses said or wrote."

Considering most of the topics were metaphysical in nature, it's hardly surprising that there wouldn't be much around to contradict things said by either. That said, if you take the creation stories in Genesis literally, we're imbred to an impossible degree. If I recall correctly, it takes 24 pairs of unrelated humans to have enough diversity to ensure that children are not born with defects at a rate higher than what's to be expected naturally. If we're all decendents of two humans, then all the genetic malformities we've picked up along the way are the result of mutations. Mutations invariably result in natural selection; the driving force behind the ToE. That one just came full circle. :)

"The context of your posting was in terms of Christianity. My reply to you is in the context of Christianity, also."

My posting was in the context of a person of faith who doesn't put on religious blinders to the world around them. If we've been given a natural curiosity and desire to explore and understand, and we've been given the intellect that makes that possible, then it's tough for me to see how our creator would want anything but for us to find out every little thing about the world around us. Faith in Christ and His teachings and the ToE are not mutually exclusive - so said the recently deceased Pope John Paul II.

"He is far more that just “a messenger.”" Mark 1:2 "As it is written in the prophets, Behold, I send my messenger before thy face, which shall prepare thy way before thee."

"Jesus Christ affirmed Moses’ creation account as part of a response to a matter posed to Him about a question of law."

We disagree on this, and this is where the crux of the issue lies. Nowhere does it state that Jesus identified Moses as the author of the creation stories we now read in Genesis. It's quite a leap to get to that point, in my opinion, based on the words given to us.

"I think you have a problem with what Jesus said about his own Creation, because you do not appear to believe His own words about the subject."

I believe we disagree on what was meant by the words in the text, that's all. Christ would be the only one who can clear that up with absolute authority. In the end, neither of us has His authority on what he meant by His own words.

"Speaking of the commandment regarding observing the Sabbath: Exodus 20:11: “For in six days the LORD made heaven and earth, the sea, and all that in them is, and rested the seventh day: wherefore the LORD blessed the sabbath day, and hallowed it.”"

Nice try, but that's not the law, but rather the explanation behind it. Quite the oddity, isn't it, that Deuteronomy 5 makes no mention of the creation stories, but instead reveals the reasoning for the Sabbath Commandment to be the deliverence from the slavery in Egypt... Of course, I suppose that two different authors might have two different ideas regarding the reasons behind a Commandment, but that'd be silly because there's just one author, right? Poor Moses; so confused... :)

"Jesus links Himself directly to the credibility of the writings of Moses."

He says He's the one Moses wrote about and that anyone who believes Moses ought to believe Him. Speaking to the audience he was speaking to, whatever texts had been ascribed to Moses at the time would be referenced by anyone appealing to that authority. Regardless of which books were or were not written by Moses, it'd be ridiculous for Jesus to waste time making factual corrections when the message was clear, correct, important, and the entire reason for His being there. He could spend His 30-year life span correcting misquotes, misascriptions, and typos, and then slide into obscurity as the village madman, or He could make use of what He had (a good message) and do what He was intended to do as the Messiah and the messenger of God, which was to save humanity both here and in the Heavens by conquering death.

"We’ll take it then that your answer is, “no,” you do not believe the writer of the Ten Commandments"

I submit that your conclusion is based on a faulty premise because your original question was worded in such a way that it made assumptions with which I disagree.

"Jesus Christ is God, therefore He is perfect as is His opinion of the words He inspired Moses to write. Will you stand there and question Christ’s own credibility on this matter?"

Jesus was a human being, born to a woman. He stubbed his toe, bumped his head, and did all the other little things human beings do. If Jesus were perfect, He'd be just God and not human at all. Human beings are defined by our imperfections. However, that's being rather nitpicky, as we'd agree that when speaking on matters of faith and God, He would have been infallible.

"Genesis was written by Moses. Jesus Christ says as much."

Please cite the passage where Jesus states, "Moses wrote the book of Genesis". Everything else is inference and assumption rolled into a ball of uncertainty with which I disagree.

"Moses also wrote Exodus."

This is a statement, not an argument. If you've got a polaroid of him writing it, please post it. Otherwise, please cite something which specifically and without ambiguity identifies Moses as the author of Exodus.

"You have been shown where the book of Exodus clearly says the finger of God wrote the actual Ten Commandments. Six literal days’ creation account is Jesus Christ’s own choice of words. It is a statement of fact in God’s own words."

So when Moses wrote Deuteronomy, he was just having an off day? Maybe he just forgot? No, he remembered to put in the explanation for the Sabbath... But he said it had to do with Egypt...

"Just admit that you choose not to believe Jesus Christ. If you won’t admit it outright, we’ll let your sophistry speak for itself."

I disagree with what you believe He meant. You can call me names all you like, but that's about the last thing that's going to change my mind.

"Jesus Christ is God, therefore He is perfect as is His opinion of the words He inspired Moses to write."

The message, being the important part of the whole thing and the reason the words were written, was kept right by the influence of the Holy Spirit. Ergo, when Jesus speaks to the message, which He often did, His opinion was that it was correct, which it is.

"Bluntly speaking it’s a yes or no answer. Either you believe Him, or you don’t."

I have no problem with the words of Jesus; I sometimes have a problem with what human beings take those words to mean. :)
118 posted on 04/13/2005 11:25:43 AM PDT by NJ_gent (Crouch down and lick the hand that feeds you; and may posterity forget that ye were our countrymen.)
[ Post Reply | Private Reply | To 100 | View Replies]

To: Ichneumon
A few good links would have been nice. Clearly you are passionate about the subject. Or perhaps it would be better to say you are quite the Darwin zealot. Back in the 70s we were concerned about global cooling, the VOLUMN of "evidence" was overwhelming and convincing with plenty of backing by the scientific community at large. How silly it all seems now.

If we go even farther back, you can find a huge body of "evidence", by the prominent minds of the day that blacks were in fact not human at all. How sick this looks now.

Are our scientists/biologists so much smarter today then they were then? Have scientists finally conquered viewing the world without any bias or preconceived notions of their time. I doubt it, and history is overwhelmingly on my side for this one.

The Bible has plenty to say about who we are as mankind, explaining why we think and act the way we do (explaining your Darwin zealotry) and it has held up against far more assaults than Darwin. I will stick with the word of God, it does not return void.

ASV Job 38:4Where wast thou when I laid the foundations of the earth? Declare, if thou hast understanding.

When all else fails, read the instructions (CCEL > Bibles and Commentaries)

119 posted on 04/13/2005 1:07:06 PM PDT by isaiah55version11_0
[ Post Reply | Private Reply | To 104 | View Replies]

To: Ichneumon; E-Mat; PatrickHenry; 3dognight; <1/1,000,000th%; Agamemnon; ClearCase_guy; ...
That's more like it.
But this thread has probably already been abandoned before I could respond.
The endogenous retroviruses sounded the most convincing, but, like much supporting evidence for evolution, the support itself all seemed based on evolutionary assumptions and sometimes circular arguments. The main evolution assumption is that similarity must indicate common ancestry, whether it be morphology, behavior, DNA fragments, etc. In the case of endogenous retroviruses, the assumption is that all the "junk" DNA that looks like virus DNA must be endogenous retroviruses. This overlooks the idea that viruses themselves originate from fragments of living organism DNA, creating a sort of chicken or the egg dilemma.

I won't deny that there is endogenous retrovirus material in animal and human DNA, but I do not see conclusive proof that any of the DNA we have in common is in fact endogenous retroviruses. In fact, I read of many indications that those suspected fragments may not be what they claimed.

The following is an extract that tells me that the endogenous retrovirus support of evolution is probably not as clear cut as you made it sound, because all that "junk" DNA is not necessarily so:

2. Don't endogenous retroviruses show evolution is true and design is false? Endogenous retroviruses are thought by many to be a type of noncoding "junk-DNA". Those who rely upon a Talk.Origins FAQ might be misled into thinking that vast amounts of junk-DNA in our genome somehow provide solid evidence that evolution (specifically, common descent) is true, that we share an ancestry with other primates, and that design is somehow falsified. However, any discussion of genetics and molecular biology needs to stay up-to-date and realize that recent advances in our knowledge of molecular biology are increasingly discovering more and more function for "junk-DNA" such that usage of the term "junk-DNA" is almost becoming taboo.

Ever since scientists began to understand the working of genetics, it became apparent that only about 3% of our DNA is composed of genes that code for proteins. Many evolutionists have claimed that the rest of the DNA is “junk-DNA," an evolutionary relic of ancient discarded genes. Not only do they claim it is a fulfilled prediction of evolution, but it is seen as a non-functional product that an intelligent designer wouldn’t create. The question at Dr. Rana's talk had to do with a type of DNA called "endogenous retroviruses" which are, according to the "Evolution Wiki" (which was entirely produced by many pro-evolution individuals at TalkOrigins) defined as: "vestiges of ancestral viral infection that have been incorporated into a host's genome. ERVs are identifiable due to the presence of sequences that code (or once coded) for viral proteins, including gag (structural proteins), pol (viral enzymes), and env (surface proteins), as well as tell-tale LTRs." ( In recent years, more and more types of “junk-DNA’ have been found to have function. If this trend continues, perhaps eventually most DNA will be found to have function. Even if some DNA turns out to not have function, it is possible that it was still designed because some DNA may have lost its function since being designed. However, endogenous retroviruses themselves have not escaped this finding of function.

The Institute for Molecular Virology apparently has a lab studying human endogenous retroviruses. According to their lab's webpage, they are studying, and finding, functionality for human endogenous retroviruses: Endogenous retroviruses (HERVs) are a major component of the human genome. Comprising about 8% of the genomic DNA, they exceed by far the number of protein-coding gene sequences. Whereas the structural genes of most HERVs have been inactivated during the course of evolution, their 600 000 - 700 000 LTRs still contain functional regulatory elements such as promoters, enhancers and transcription factor binding sites and are able to modulate the expression of adjacent cellular genes. The aim of our experiments is to elucidate the biological function of HERVs, their involvement in evolutionary processes and their possible role in the development of disease.
Research focus
Expression and function of endogenous retroviruses in human neoplasms and autoimmunity
Activation of retroviral genes by environmental factors
Control of gene expression by HERV regulatory sequences (LTRs)
Construction of tissue-specific retroviral vectors based on HERV LTRs

While their website assumes that the origin of HERVs is ultimately evolutionary (as they would assume for the origin of any functional or allegedly non-functional strand of human DNA), the important point is that they are finding function! This finding of functionality could make more sense under an intelligent design perspective, where HERVs are not there because of a viral infection in our evolutionary past, but because they were intended to fulfill some function in the human genome by an intelligent designer.

Indeed, even if there are still things we don't understand about endogenous retroviruses, consider the following examples of types of DNA which were once thought to be "junk" but now are not. This might encourage people looking at "junk-DNA" to take a "wait-and-see" approach, as more and more types of junk-DNA seem to be being discovered all the time:

120 posted on 04/13/2005 4:27:40 PM PDT by E-Mat
[ Post Reply | Private Reply | To 104 | View Replies]

Navigation: use the links below to view more comments.
first previous 1-20 ... 61-8081-100101-120121-132 next last

Disclaimer: Opinions posted on Free Republic are those of the individual posters and do not necessarily represent the opinion of Free Republic or its management. All materials posted herein are protected by copyright law and the exemption for fair use of copyrighted works.

Free Republic
Browse · Search
Topics · Post Article

FreeRepublic, LLC, PO BOX 9771, FRESNO, CA 93794 is powered by software copyright 2000-2008 John Robinson