Evolution Vs Creation

[Hambone]

Using Copy Errors to Reconstruct Evolution

A Fable

Once upon a time, in a faraway land long, long ago, there was a monastic order whose mission was to preserve and spread its sacred writings. Every young monk had to spend years hand-copying these texts, then leave the monastery with his writings, travel, and found a new monastery. Novices at the new monastery, in turn, would recopy the founding monk's manuscripts by their own hand, and subsequently take these as they each journeyed on to found their own monasteries.

 

Not all copies were flawless, however. Occasional mistakes were made, where a letter was carelessly copied incorrectly, or a word or phrase accidentally deleted. Over time, the writings at different monasteries came to differ in a number of particulars. Each monastery had only one complete copy of the text, and there was no "standard reference" to decide which (if any) was the "original" text. There came a time when monks from different monasteries began to quarrel bitterly over the validity of each others' texts, each claiming that theirs was the one "correct" version.

 

A wise Queen ascended to the throne of this land, and she became concerned about the impact that the monks' quarrels were having on the peace of her region. "Bring me these writings, that I may see for myself what you are arguing about!" she proclaimed. The monks complied, and she began examining the texts side by side.

 

Here are four of the excerpts she examined:

 

 

There is but one who declares motherwise loves. (Monastery A)

There is but one true God, and he who declares otherwise flies. (Monastery

There is not one true Good, and he who declares otherwise lies. (Monastery C)

There is not one true God, and he who declares otherwise dies. (Monastery D)

"But this is silly!" she exclaimed. "I don't believe a single one of you has the correct ancestral text. Your texts seem to differ in three ways, all of which were probably the result of errors made while copying these texts from previous versions."

 

Some errors are due to the insertion or deletion of a single letter. For example, two of your texts list the word "God," but one of them lists "Good." It looks like someone accidentally inserted an extra letter "o" to turn "God" into "Good."

Some errors are due to changing a letter. For example, the word "dies" occurs in one text, and the word "lies" in another text. I'm pretty sure one of these is the original word, and the other is a mistake made by incorrectly copying the first letter. My guess is that "lies" is the original.

A third type of error is the accidental deletion of a whole line. For example, the text from Monastery A is missing the phrase "true God, and he", which is found in some form in all the other texts. Probably the monk copying this phrase skipped a line. I would count that as a single mistake, not an accumulation of many single letter deletions, because that is the simplest explanation.

 

 

"Futhermore, I can make a reasonable guess as to how your texts might have diverged over time. Would you like me to show you how?" The monks scratched their heads, looked at the four texts, and replied, "Yes, your highness. Please show us how this could be."

 

 

"Let us proceed as follows," she said. "Arrange all four fragments one under the other, so that we can align individual letters." [Note: On a computer, use a non-proportional font such as Monaco so that every letter has the same width.]

There is but one who declares motherwise loves. (A)

There is but one true God, and he who declares otherwise flies. (

There is not one true Good, and he who declares otherwise lies. ©

There is not one true God, and he who declares otherwise dies. (D)

 

 

"Now color all letters that differ from others in the same column. Let us also be free to move any text to maximize its alignment with the others, even if this means introducing gaps or extra spaces:"

There is but one who declares motherwise loves. (A)

There is but one true Go d, and he who declares otherwise fli es. (

There is not one true Good, and he who declares otherwise li es. ©

There is not one true Go d, and he who declares otherwise di es. (D)

 

 

"We can now estimate the number of copy errors that separate each message from the other three. I'm going to assume that the original, or 'root' text, which none of you possesses, reads:"

 

There is but one true God, and he who declares otherwise lies.

"If this indeed the 'root phrase,' then each of your texts then could have originated as follows:"

 

(original)

(error 1: 4 words deleted)

(error 2: addition of "m")

(error 3: insertion of "v")

(error 4: "i" ---> "o")

 

(original)

(error 1: insertion of "f")

 

(original)

(error 1: "b" ---> "n")

(error 2: "u" ---> "o")

(error 3: insertion of "o")

 

(original)

(error 1: "b" ---> "n")

(error 2: "u" ---> "o")

(error 3: "l" ---> "d")

 

Text A: 4 errors removed from original

There is but one true God, and he who declares otherwise li es.

There is but one who declares otherwise li es.

There is but one who declares motherwise li es.

There is but one who declares motherwise lives.

There is but one who declares motherwise loves.

 

Text B: 1 error removed from original

There is but one true God, and he who declares otherwise lies.

There is but one true God, and he who declares otherwise flies.

 

Text C: 3 errors removed from original

There is but one true Go d, and he who declares otherwise lies.

There is nut one true Go d, and he who declares otherwise lies.

There is not one true Go d, and he who declares otherwise lies.

There is not one true Good, and he who declares otherwise lies.

 

Text D: 3 errors removed from original

There is but one true God, and he who declares otherwise lies.

There is nut one true God, and he who declares otherwise lies.

There is not one true God, and he who declares otherwise lies.

There is not one true God, and he who declares otherwise dies.

 

 

 

"I've made several assumptions," said the Queen.

Errors occur one at a time.

An error can involve a single letter change, insertion or deletion of a single letter, or deletion of a number of letters or words at a single time.

The shortest number of errors between two messages is most likely to have occurred (the principle of parsimony.)

 

 

 

 

"I may have erred slightly--for example, in 'text A' I arbitrarily listed the four-word deletion as the first error, when it could equally well have been the second, third, or last. But I have always picked the shortest error path to get from ancestral text to each of your texts. So the number of errors is, in a way, a measure of the evolutionary history of your texts."

"Furthermore," said the Queen, "I can even create an 'evolutionary tree' to illustrate how your texts have evolved. I'll let the number of errors be proportional to distance along a line. Then the history of your texts looks like this:"

 

 

"Note that monasteries C and D must have shared the same text until very recently, whereas monastery A has a long separate history."

 

Keep Reading...

[Hambone]

Rooted and Unrooted Trees

"This is wonderful," exclaimed the monks. "So we now know the true original message, at the base of this tree!"

"Yes," replied the Queen, "but only because I knew all along what that message was. You see," she said, pulling a scroll from her desk, "here is the original scroll, signed and dated by the monk who founded your monastic order long ago. It was given to the monarch of that time for preservation, and has been kept safe and unchanged in this palace all that time. Since we know its content, we know the root of the tree, and can place the branches in correct order."

 

"But what if you did not possess that scroll?" asked the monks. "Could you still have deduced the correct ancestral text?"

 

"No," answered the Queen. "If the only copies I had to work with were your differing manuscripts, our problem would be much more difficult. Lacking knowledge of the ancestral phrase, we would have to compare each of your messages to see by how many errors they differed from each other. We could still construct a tree, but it would have to be an 'unrooted tree,' since we did not know the true root message."

 

"For example, comparing messages C and D, we would find that they differed by only two errors:"

 

There is not one true Good, and he who declares otherwiselies. ©

There is not one true Go d, and he who declares otherwise dies. (D)

 

 

"However, A and D would differ by at least seven errors, if we count the deletion of several words as a single error, along with letter changes and insertions or deletions:"

There is but one who declares motherwise loves.(A)

There is not one true God, and he who declares otherwise di es.(D)

 

 

"We would also have to measure the minimal error distances between A and B, A and C, B and C, and B and D. Then we would have to draw all possible error trees to find which one was the most parsimonious. Frankly, it's a monumental task."

[Hambone]

Commentary on the Fable

In our day, we are fortunate to have computers available, since they offer by far the most practical way of constructing error trees. Unrooted trees can be represented in a variety of ways, such as:

We can devise two type of "error trees," which might better be called "phylogenetic trees" since they illustrate the evolutionary relationships among our objects of study:

 

 

Rooted trees, where extra data allows us to identify the ancestral phrase or organism. In Biology, fossil data can allow rooting of some trees.

Unrooted trees, where we lack data about the true ancestor, and must infer relationships by making comparisons between our phrases or organisms.

[Hambone]

Nucleic Acid Sequence Comparisons as Measures of Evolutionary Separation

In the Fable about monks disputing the authenticity of their texts, we explored the use of copy errors to predict something about evolutionary lineages. A somewhat analogous process can be used to compare nucleic acid sequences and infer something about their evolutionary history.

DNA encodes the information for genes. DNA is reproduced with great fidelity during replication and repair, but occasional copy errors occur, with frequencies between 1 in a million and 1 in 100 million. For example, normal DNA replication would always place a thymine (T) base opposite an adenine (A) base, and a guanine (G) base opposite a cytosine © base.

 

 

Occasionally, however, a mistake will occur, leaving a mispaired base. After another round of replication, the mistake will be "locked in" to one lineage of progeny cells. Such heritable mistakes are called mutations. In the example below, cytosine © is accidentally inserted when replicating from an adenine (A) template, instead of the normal complementary base thymine (T). After one further round of replication, the new C base has acted as a template to insert guanine (G) into newly replicated DNA, so the mutation is "locked in." No trace of the original A-T base pair remains.

Not all mutations survive. If a mutated gene is critical to the cell and functions poorly in comparison to the non-mutated gene, mutant progeny may fail to survive, and the mutant gene is eliminated from the population. Some mutations do survive, however, and these tend to accumulate with the passage of time.

Nucleotide differences between different DNA molecules provide an astonishingly useful way of measuring evolutionary distance. No fossils are required. One assumes that, if two comparable genes or DNA segments have nearly identical nucleotide sequences, then they shared a common ancestry in the recent past. By contrast, if they differ significantly in many nucleotide positions, their lineages must have diverged long ago.

[Hambone]

Example: Using DNA Sequences to Construct an Unrooted Tree

The following example shows how an evolutionary tree is constructed for four hypothetical organisms whose DNA sequence in one homologous region is known.

 

 

AACGTCGAAA (Organism A)

AACCTCGAAA (Organism

AGGCTAGAAA (Organism C)

AGGCTAGTAA (Organism D)

 

A and B differ by one base substitution. C and D also differ by one base substitution. But A and C differ by three substitutions, and A and D by four. B and C differ by three substitutions, and B and D also by four. In terms of evolutionary history, A and B appear to be very similar,as do C and D. A-B and C-D are more distantly related.

Since we have no clue about their ancestors from this data, we cannot draw a rooted tree (see Rooted and Unrooted Trees in the previous page if you don't remember this distinction.) We can draw an unrooted tree, letting a computer determine the best data. Here are a couple of ways of drawing such a tree:

 

The choice of line shape is quite arbitrary. What is important is that linear distance between organisms is proportional to the number of base substitutions. Although we assume that these distances are correlated with time, we don't know how frequently mutations occur, so we can't equate distances precisely with time. If organism B differs from C by three times as many nucleotide substitutions as it does from A, we can't assume that C diverged from A exactly three times as long ago as B did from A.

[Hambone]

Ribosomal RNA Genes as a Yardstick for Evolution

Scientists have learned that mutations occur far more frequently in some genes than in others, judging from the number of nucleotide substitutions that can be found by comparing different organisms.

If you were interested in studying the evolutionary relationships of a group of closely related species (such as humans, chimpanzees, and gorillas), where evolution has occurred within the past 20 million years, you would probably want to examine a gene that mutates frequently, so that you could find some differences to study. But if you were interested in comparing living creatures over a time span as long as 4 billion years, you would be better off choosing to study a gene that mutates only rarely.

 

What gene(s) mutates most slowly in organisms alive today? Possible candidates for this honor include the genes for ribosomal RNA.

 

Cells produce three distinct types of RNA molecules:

 

 

Messenger RNA (mRNA), which carries genetic information to ribosomes in order to specify the structure of proteins. Bacterial cells may contain many hundreds of different types of mRNAs at any one time. They account for only about 5% of total cell RNA.

Transfer RNA (tRNA), which carries amino acids to ribosomes in order to provide the building blocks for growing proteins. Bacterial cells may contain about 60 different types of tRNA, accounting for about 15% of total cell RNA.

Ribosomal RNA (rRNA), which is part of the structure of ribosomes. (A short Tutorial on Ribosome Structure reviews relevant concepts in case you need to refresh your understanding of ribosomal RNA.) Bacterial cells often devote as much as 90% of their energy to synthesizing new proteins, and require large numbers of ribosomes. rRNA accounts for about 80% of total cell RNA.

The genes for ribosomal RNA are among the most stable and unchanging genes known. Viable mutations do occur, but infrequently. In particular, the genes for the small subunit RNA (16S in prokaryotes, or 18S in eukaryotes) have been used extensively to compare living organisms as diverse as bacteria, mushrooms, and humans.

 

In 1977, Carl Woese of the University of Illinois and colleagues astonished the scientific world by publishing results of their extensive studies of small ribosomal subunit RNAs (Proc. Natl. Acad. Sci. U. S. A. 74:4537, 5088.) Predictably, they found wide differences in the RNAs and RNA gene sequences of bacteria and eukaryotes. What was so surprising, however, was their discovery of a third group of organisms, the Archaea, whose RNA sequences were as different from other bacteria as they were from eukaryotes. These differences are summarized in the following unrooted phylogenetic tree (redrawn from Woese et al.)

Archaea share much more 16S RNA sequence homology among themselves than they do with either the other bacteria or the eukaryotes. Based on these studies, Woese suggested abandoning the traditional division of all living organisms into five kingdoms:

Monera

Protista

Fungi

Plantae

Animalia

 

 

Instead, Woese proposed grouping all living organisms into three domains:

 

Bacteria (the eubacteria, or "true" bacteria)

Archaea (the archaebacteria)

Eucarya (the eukaryotes)

 

 

Scientific reaction to this proposal was mixed. Everyone agreed that the Archaea seemed even more unrelated to ordinary bacteria than had previously been thought. But there was skepticism about the wisdom of entrusting the most fundamental taxonomy entirely to the results of a single methodology, based on comparing only ribosomal RNAs. What if future studies should reveal that ribosomal genes evolved quite differently than other genes? To many, it seemed wiser to wait and see what would be revealed by further study, particularly the sequencing of complete genomes of Archaea.

[Hambone]

The Genome of Methanococcus jannaschii

So far, our focus in this activity has been to use sequence comparisons as a way to estimate evolutionary relatedness. We've seen that, by using 16S rRNA gene sequences, we could clearly identify Archaea and Bacteria as two separate groups of organisms. We've also seen, in Part I of the activity, that Archaea and Bacteria differ greatly in their physiology. What we have not yet seen, however, has been evidence that the entire genomes of Archaea (not just the ribosomal RNA genes) are very different from those of the Bacteria. Until 1997, no archaeal DNA had been completely sequenced.

Methanococcus jannaschii was isolated in 1982 from the ocean floor at a depth of 2600 meters (8500 feet), at the base of a hydrothermal vent. The organism is named after Holgar Jannasch, a microbiologist from the Woods Hole Oceanographic Institute, who pioneered the exploration of hydrothermal vents as microbiological communities, using the deep sea submersible vessel Alvin. Such vents occur in regions of sea floor spreading, where hot magma underlying the sea floor comes in contact with seawater seeping into the cracked rock. The water becomes heated and takes up chemical compounds, such as hydrogen sulfide and carbon dioxide, which can stimulate microbial growth. M. jannaschii is an archaeon, growing optimally at a temperature of 85 oC and, as its name implies, produces methane.

 

Methanococcus jannaschii contains about 1.6 million base pairs of DNA, a fairly small size, which made it an attractive candidate for gene sequencing. The scientific report of this sequence was published in August, 1996 (Science 273: 1058-1073). The complete genome sequence is available on the Web at the TIGR (The Institute for Genome Research) database.

 

 

The genome of M. jannaschii contains three distinct elements:

Description Size (base pairs) Predicted coding regions (ORFs)

Circular chromosome 1,664,976 bp 1682 proteins

Large circular DNA element 58,407 bp 44 proteins

Small circular DNA element 16,550 bp 12 proteins

Total

1738 proteins

 

One of the first things the researchers did after obtaining the sequence was to predict all sections of the genome that coded for proteins. This is done by programming a computer to look for open reading frames, or ORFs. (If you are not familiar with ORFs, see the short Tutorial on ORFs.) Once each ORF is found, computers compare its predicted amino acid sequence with other known proteins, looking for similarity. If, for instance, a protein from M. jannaschii corresponds in 73% of its amino acids with a certain enzyme required for RNA synthesis from E. coli, then the computer identifies the M. jannaschii gene as a predicted RNA synthesis gene. Some ORFs cannot be matched up with any known proteins in current databases; these are called hypothetical proteins.

[Hambone]

That's enough for now. Upon request I will post more.

[Playaa]

Hambone, about your "forbidden post" God is REFERED to as a man because it gives him familiararity(sp?) If we referred to God as "IT" he wouldn't seem so familiar.

 

how about this Hammy-ole-boy

God loves me, she sent her son to die on the cross for my sins so that I would be saved.

 

as to all the other posts, I have yet to read them and hopefully will get the time to read them, but I probably won't be able to refute them seeing as how I'm not as based in science as you seem to be.

But I would like to say that even though you won't admit it, Evolution is based on Faith, it's your faith in man. You personally cannot know the facts except through other men.

[Playaa]

hambone, I'd like to know where you got all that information from?

I'm assuming you just copied and pasted from a website since the posts are so close together....

 

I'd actually like to take this argument back down to the majority of the worlds level......

why don't you tell me how a monkey became a man.....?

[Hambone]

Evolution is based on facts, not faith. You are fundamentally wrong. Monkey also didn't evolve straight to man. I don't think you read everything I posted.

[Playaa]

no I already said I didn't read it.....

 

I meant tell me how the monkey became man, all the steps....

but I take it back

I don't wanna hear about it........because no matter what happens. no one is going to change thier views

even if you know so much more about science than I do that you can provide me with arguments I can't refute you are not going to change what I know about this life. And that is that God exists, and since he exists I have the faith that the Bible is his Divine word through men. I will say that you know more about science than I do. So I will concede that an argument with me (and probably Rev) would make it seem as if you had beaten all Creationists. I'm not smart enough to argue with you, find a worthy opponent. I'm sorry I've failed but it's the honest truth, I would only hurt Creation more by trying to argue it with you.

 

I would hope that no hard feelings are felt by you or Rev towards one another.

 

You have however led me to want to study creation/evolution more. So hey, if you're right then you've just converted someone then....

but if not, maybe one day we'll continue this more.....

 

for now I withdraw....

[Hambone]

I thank you for your kind words then. In return I promise to reread Genesis.

[Guest Mossad]

hambone u never answered my question....why are you so angry at the church?

[Hambone]

The following is merely a theory of mine. I think there is only one true emotion. Hate. I won't explain this here, because that was not the question. I was taught Christianity, and I believed it. After awhile, science came into my life. It taught me real truth, stuff that I can prove, stuff that is real. Church lied to me. Betrayal spawns Hate.

 

Did you really want to know that?

[Guest Mossad]

yah...but if religion makes someone a better person, what can you possibly have against it?

[Cyklik]

There is no such thing as hate if it cannot be contrasted. And to contrast it, you need some other frame of reference. You guessed it! Love! Without love there is no such thing as hate, and likewise the other way. Sorry man, there's no other way it can happen.

 

___________Edit___________

I think it would seriously be nice if this whole evolution/creation thing simmered down, since we obviously cannot agree on many points at all. While I respect your views, I don't share them. I just hope that you can feel the same way. Let's be mature about this.

[Jiffy]

wow hammy...deep

[Guest the mack]

science came into my life. It taught me real truth, stuff that I can prove, stuff that is real. Church lied to me. Betrayal spawns Hate.

hambone is a very smart person....does know how many people have killed in the name of their releigion??? thats right how many people have died because of they didnt believe in christianity.....and how could the church be so corrupt (molesting of young boys by pastors)

 

 

because of releigion stem cell research is hindered and certian dieases were

because of releigion Galieo was forced to give up his ideas about the universe and accept that the earth is the center of the universe (there are fundmental christians that still believe this)

becuase of releigion abortion is "evil" and now some abortion doctors have been murdered by christians (in the name of god too eh?), 14 year old girls keep their children and raise them (it is a proven fact that if your mom was a teen pregancy then you have a much higher chance of being a teen pregancy yourself)

because of christians the mouring after pill was delayed for years from coming out which prevents pregancy; without causeing an abortion!!!

 

i have many more of these and im just to lazy to post them (omgosh run away lazyness is a sin too)

 

does anyone know that by playing counterstrike you are breaking on of the ten commandments??? figure out which one u church going folks

[Hambone]

A man was burned in 1320 for denying the Ressurection. Burned to death. Why was he not the savior of humanity, he died for his views on Christ and god?

[Hambone]

Mossad, religion does not make everyone a better person. Religion is a loose cannon. It justifies great deeds and wicked ones. Religion causes the biggest atrocities in human history. September 11, to use a recent example.

[Playaa]

I can wholeheartedly agree with Hambone on this one....

religion doesn't make someone a better person, and it IS a loose cannon and ppl use it for their own greedy wants and desires.

 

however, the majority of us fighting for what ppl refuse to stop calling "religion" are actually Christians.....

 

to make it more so you can understand it.......

when someone tells me that I'm a moron for following religion and for believing in a religion because of all those evil things done.......it's like me saying, well the mack plays Counter-Strike and a large majority of CS players are cheaters, so he must be a cheater also.

 

now real counter strike players know that only a few (well alot but still not the majority) of cs players are cheaters, however the rest of the non CS playing world sees the few evil morons and hears about their cheating exploits and assumes we all do it.

Just like ppl assume I'm going to go out and shoot someone because I play lots of violent video games.

 

So when you bring up all those points to disabuse religion and especially Christianity, think about it from that perspective, that those are a small minority of ppl that don't understand the truth of this "game" we call religion

[MC_Ranger]

I just scanned through pages and pages of posts from Hambone.

 

While I'm sure he is a very smart kid, please don't equate cuts and pastes of other peoples' thoughts and research into intelligence.

 

Hambone is blaming religion for all the bad things that happen in this world and when somebody calls him on it, he flings words like "Nazi" around.

 

Everytime he comes up with a solid point, he taints himself with phrases like "religion is for the weak". I, personally, cannot take anything he says seriously. He is hostile and offensive and uses "truth" as a flimsy shield. If he hasn't already, I'm sure he'll hollar about "freedom of speech" and maybe throw a reference in about Martin Luther King.

 

I'm going to refrain from joining this "debate" because that would lend credibility to a topic that really has no place in this particular forum.

 

You can tell by the tone of his posts and his hostility toward religion/God that he is trying to come to grips with some personal issues. I hope his suffering ends soon because, at 17, you have a long way to go and if you're not careful, you will end up full of the only emotion you claim exists.

 

I'd just assume see this post deleted from this forum. It has gotten out of control and doesn't belong.

 

Ranger

 

P.S. I'm already an Evolutionist, so don't waste your time replying with more religious-like preaching of science.

[Guest the mack]

that would lend credibility to a topic that really has no place in this particular forum.

what forum does it belong in?

 

you do though have really good points on saying that not all christianty is evil which i 100% agree with u....most of what releigion how taught us is great (meaning do not kill anyone or be nice to your neighbor) but the ....how do i say this...the relegion part of releigion (wow that makes sense) is just been proven time and time again to be false

[Playaa]

that's the funny part...

the "religion part of religion" (being the faith in a god and such I would assume) can't really BE proven wrong until the end of the world now can it?

 

the only way to know the true answer....is to die....

 

Death, the 100% prove of whether God exists....