Feedback for the week of June 6, 2005

Presuppositionalism vs evidentialism, and is the human genome simple?

Dear AiG,

Recently I’ve come across quite an interesting piece on the complexity of our genes, and as much as I hate to admit it, my faith is wavering due to this. It is the following…

‘The evolutionist refutation of this that I have heard so far is that “it is incorrect” to assume that all the enzymes, little mechanisms etc must be functioning perfectly in order for the cell to live. But nobody that I have found has explained why this is so. I would like some one on here to elaborate, please.

I can handle this one in pretty good detail

Let us first lay down some structure for the description.

Let’s say for simplicity that there are 3 billion base pairs in a DNA sample.

The DNA sequence doesn’t work by a certain base pair corresponding to a certain Amino Acid but a 3 base pair codon as seen here:

DNA can’t be thought of as a mechanism that is 3 billion “letters” long but as 1 billion “codons” long. You would now probably think that this corresponds to 1 billion amino acids to make all of the proteins right? Well it takes a lot more than that for it to work actually. So let us begin to describe how we go between these languages.

So let’s begin with the creation of RNA

RNA Polymerase is what will form the RNA, but how exactly does it know to form it? Well it needs a promoter sequence that screams out “Hey come over here and copy this!” and are usually found near the start point, but there are also enhancers/silencers that effect this process and found 1000’s of base pairs away! To continue, RNA Polymerase will encapsulate a segment of DNA and move along it making base pairs to correspond to the DNA with he help of a bunch of proteins. So DNA contains a lot of promoter, enhancer, and silencer sequences that are not incorporated into the proteins and also do not have to be perfectly formed to truly function. Also, somewhere along the path of the formed RNA is a junk region, an Intron, that just gets snipped out of the sequence.

So now we have a completed RNA for a protein, the thing with this is that while we prefer for this sequence to be correct and all, it doesn’t have to be perfect. If 3 codons wound up missing it doesn’t really cause much of a problem in general, and if a wrong codon is present then it could still code for the same amino acid or one similar enough to code for a similar protein

So now we have tRNA swoop in with an attached amino acid and connect along the mRNA and attaches all the amino acids together in a chain to make a protein in a process that I don’t want to get into right now. Needless to say that all the amino acids are hooked up and then some modification occurs and the protein is folded.

So now back to the original question: The evolutionist refutation of this that I have heard so far is that “it is incorrect” to assume that all the enzymes, little mechanisms etc must be functioning perfectly in order for the cell to live. But nobody that I have found has explained why this is so. I would like some one on here to elaborate, please.

So far from your understanding is that it is has to be correct…so let us educate you!

First there are large amounts of repetitive DNA sequences that don’t code for anything at all and aren’t a promoter/enhancer/silencer and don’t really affect you at all. Unique DNA is only 64% percent of the total.

Next if you have an “error” in one sequence it probably isn’t detrimental, since it will most likely code for a similar protein.

Then there is the fact that multiple enzymes perform the same roles in the cell and the body and if one of these isn’t formed then it really doesn’t matter since you have other enzymes that fulfill the role.

So, in most cases errors in the system aren’t as doom bringing as one might think, although in some very rare cases they can be. Even in your body there are probably a few copies of DNA with a mutation or two but, there are enough proofreading factors to repair it all anyway.

To end a little math fun!

3 billion bases=1 billion codon language

64% of 1 billion codons is 640 million codons that are unique

640 million codon “symbols” that have 21 meanings, 19 amino acids, a 20^th amino acid that means start, and a stop single.

So when you think of it as a 640 million codon text with just 21 “words” it doesn’t seem so complex does it?”

-Thats the end of it. When it’s broken down so simply, evolution seems to be more possible that way, I can’t seem to find any errors either, I was hoping that you may be able to help me regain my faith by showing me, as well as anyone else who reads this, the errors within, which I certainly hope there are.

In Jesus’ Name,
E.P.
USA

---

Dear AiG,

Recently I’ve come across quite an interesting piece on the complexity of our genes, and as much as I hate to admit it, my faith is wavering due to this. It is the following…

I will address the specifics below. But first I must urgently counsel you that your faith is misplaced if it is wavering because of such matters. One’s faith should never be based on specific examples of design, but on God’s Word. Your problem is what my colleague Andrew Lamb called the ‘evidentialist roller coaster’—where one’s faith goes up and down depending on the status of the latest ‘evidence’. Or to paraphrase Ephesians 4:14: ‘tossed to and fro, and carried about with every wind of evidence.’ In fact, he informs me that it described his own life before joining AiG and learning about presuppositionalism. That is, the difference between creation and evolution is not about the evidence, but the presuppositions by which we interpret the evidence (see also Evolution & creation, science & religion, facts & bias).

I will address a few possible misunderstandings about presuppositional apologetics:

Dear Ken Ham and Answers in Genesis, Here is a word of encouragement I believe from the Lord as you obey Him in rebuilding the foundations of the walls. The word of encouragement comes from the parts of the book of Nehemiah as Answers in Genesis (AiG) is rebuilding the walls of the church in America and abroad. Nehemiah starts and ends with prayer and you find that prayer first is always his policy personally and corporately. Prayer, pain, and perseverance are the three P’s that are eminent in Nehemiah and seem to relate well with AiG in all its ministry from speaking conferences to preparing exhibits for the Creation Museum. Looking deeper into Nehemiah we can find much encouragement for the work AiG is undertaking. From the beginning of Nehemiah chapter one we see Nehemiahs genuine concern for the remnant as he asks after it. Upon Nehemiah hearing the words (words of distress and peril) he is broken hearted for God’s people and for the wall and gates and, therefore, proceeds in prayer to bring it before the Lord waiting for days for the Lord’s answer. [Ed. note: Actually, it was from the month of Kislev that he prayed and in the month of Nisan the king granted him permission to go.  That would be like from January to May for us (4 months).] The Lord God opens the eyes of his people and speaks to them who wait on Him.  God answered Nehemiahs prayer. God has spoken to AiG of the situation regarding His Church’s foundational walls being abject and derelict. He will answer our prayers. The Church has in many respects become a reproach and byword to society because it has forgotten why it is set apart and abandoned God’s word thus losing its strength and purpose. However, AiG and other creation ministries have had their hearts broken for the church by the Lord and realize the vital importance of rebuilding the walls. AiG’s Creation Museum is a big part of the wall restoration.  Nehemiah surveyed and studied the walls in furtive then presented the blueprint to the people. He was careful, calculated and took prayerful, practical steps in going about the Lords work. AiG has gone before the Lord and sought Him and He has answered and now have started the Creation Museum. The people united in the Lord, said Let us arise and build. Nehemiah didn’t have the best masonry and brick workers of his day but he had the Lord’s people united to do the Lord’s work. However, when going about the Lords work that old enemy Satan will attack with the forces of darkness. Remember the enemy doesnt need to attack strongly where their isnt a reason.  Sanballat, Tobiah, and Geshem mocked and despised Nehemiah and crew. They taunted them saying What is this thing you are you doing? Are you rebelling against the king? AiG isnt rebelling against science and the King of Kings for that matter. The true history and thus science of this world will be seen in the Creation Museum as part of rebuilding the walls. The mass media and various other evolutionary agencies and organizations will taunt and misreport the truth hoping to stop the rebuilding of the walls. However, the God of Heaven, the Creator will give us success because it is His battle, His walls, His museum, and His creation. The enemy kept trying to deter and frighten Nehemiah and company but they continuously sought the Lord and used the Lords practical measures. As you go building the walls remember to firstly keep taking everything to the Lord and secondly He will guide you into how to put practical measures into place for right living and building. Nehemiah was above reproach to his enemies, and prepared for battle should his enemies attack. May the Lord continue to keep AiG above reproach and prepared for battle as you rebuild the walls. The work was done in 52 days as recorded in Nehemiah, because it was done by the Lord. He used the obedient, willing, and prayerful then, as He does today! The wall was rebuilt in Gods time and so will the Creation Museum be. May the Lord bless the Creation Museum work and AiGs ministry in rebuilding the foundational walls of the Church. May the Lord use us all as He builds us the Church to His glory! Every blessing, Joshua VanTine Birkenhead, England

1. Evolution is not based on evidence that speaks for itself; rather, it is a deduction from their own presuppositions—a priori commitments to materialism and rejection of a designer, because they can’t bear a ‘divine foot in the door’. Therefore they have no right to object when Christians start from their own presuppositions. This is a theme of the instructive article Creation: ‘where’s the proof?’ When the person you talk to on creation insists that you ‘leave the Bible out of it’, they are really saying the deck should be stacked one way, and Searching for the ‘magic bullet’: Why do creation-defenders often seem to be too quick to jump onto the latest ‘evidences’?

2. This commitment to materialist presuppositions explains why so many evolutionists cling onto their faith, no matter how absurd the explanations. And we should remind evolutionists that Darwin maintained his faith in evolution (and in this case I mean blind faith, not faith in the biblical definition), despite the fact that there were many problems.

   For example, Darwin knew that there was a lack of transitional forms, but had faith that paleontologists would dig them up. But this faith was misplaced, as shown in The links are missing. Darwin and Huxley were also most frustrated at being unable to refute Lord Kelvin’s physical arguments against the timeframe he needed. Yet Kelvin’s argument still essentially holds (see Lord Kelvin revisited on the young age of the earth).

   Indeed, if an evolutionist is demanding that you renounce your faith unless you can answer a particular objection, then remind him that the leading evolutionists did not when they had unsolved problems. Indeed, today, so many evolutionists demand that creationists abandon biblical creation because of an apparent anomaly, but if an evolutionist can’t answer something, then it’s ‘the whole purpose of science is to solve problems.’ If that’s true, then the same allowance should be made for creationists. And obviously, the truth of Christianity doesn’t entail infallible knowledge by every Christian!

   In any case, many of the alleged proofs for evolution have been discounted, e.g. staged photos of peppered moths, Haeckel’s forged pictures alleging embryonic recapitulation and similarities, the alleged Ostraea–to–Gryphaea evolution which was merely ecophenotypic change. Indeed, when I was in high school, Ramapithecus was taught as a human ancestor, but now it’s thought to be a variety of orangutan. My boss Dr Carl Wieland remembers being strongly influenced when young when National Geographic touted Zinjanthropus boisei as a human ancestor, which is completely discounted today.

3. Accepting the biblical presuppositions is not a matter of blind faith. Biblical faith is not blind; rather, it is belief, and trust and loyalty, for sound reasons, as explained in Fallacious Faith. See also Does John 20:29 Promote a ‘Blind Faith’? because a contextually illiterate person called Douglas Yu recently wrote a letter to Nature claiming just this (Nature 435(7040):275–276, 19 May 2005). I have explained to an agnostic why it is rational to trust the axioms of Scripture. See also Apologetics Q&A.

4. We are not merely asking opponents to consider biblical presuppositions as an alternative way of looking at the evidence. Nor are we merely saying that they are ‘nicer’, nor even that they provide a superior framework that better explains the data (although both of these are true as well). Rather, the claim is even stronger: that the biblical framework is the only one that provides the foundation for science, voluntary will, logic and morality, as I explained in this feedback response.

So while a materialist may argue ‘scientifically’ about minutiae as below, his own materialistic axioms provide no basis for such an argument in the first place. So in reality, he is cutting off the branch he’s sitting on. Conversely, only the Christian axioms make science possible. Therefore, the materialist has no choice but to confirm Christian presuppositions even to prop up his attempts to attack them.

Now on to the specifics, although try in future to avoid getting bogged down in minutiae because that is allowing the opponent to set the terms of the debate. That is, it already concedes to him his faulty presupposition—the autonomy of man’s intellect—because it erroneously assumes/concedes that this intellect is neutral in its approach to interpreting the facts/evidence. That is, it confirms (fallen) man in the error of his way in placing ‘reasoning’ and ‘interpreting’ above God’s revealed Word.

‘The evolutionist refutation of this that I have heard so far is that “it is incorrect” to assume that all the enzymes, little mechanisms etc must be functioning perfectly in order for the cell to live. But nobody that I have found has explained why this is so. I would like some one on here to elaborate, please.

But this is a straw man. Certainly there is some leeway, but also a lot that must be exact, especially in the active site. You can even see this in evolutionary writings, but the code word here is ‘conserved’—i.e. the sequence was so vital that natural selection conserved it by eliminating variants. As the following conservative calculation shows, even making generous assumptions to the evolutionists (e.g. ignoring the chirality and polymerization problems), the origin of life from non-life still defies probability (from my DVD Chemicals to Living Cell: Fantasy or Science):

• 10⁸⁰ atoms in the universe

• 10¹² atomic interactions per second

• 10¹⁸ seconds in the universe, according to the fallacious big bang theory ∴ 10¹¹⁰ interactions possible.

• 20 amino acid letters

• 256 enzymes for the simplest possible life

• 10 conserved amino acids on average

  ∴ chance is 1 in (20¹⁰)²⁵⁶ = 20^–2560 = 10^{–2560.log20} = 10^–3330

• Like guessing the correct 3330-digit PIN!

• Calmodulin: 142/143 amino acids conserved: 20^–142 = 10^–185

Here is a recent paper that explains probabilities in technical detail, likewise making allowances for variants—Probabilities of randomly assembling a primitive cell on Earth.

‘I can handle this one in pretty good detail

Let us first lay down some structure for the description.

Let’s say for simplicity that there are 3 billion base pairs in a DNA sample.

Well, this is the number of base pairs of the human genome.

‘The DNA sequence doesn’t work by a certain base pair corresponding to a certain Amino Acid but a 3 base pair codon as seen here:

Yes, we know—see The programs of life.

‘DNA can’t be thought of as a mechanism that is 3 billion “letters” long but as 1 billion “codons” long.

Or as I say, three DNA ‘letters’ to one protein ‘letter’.

You would now probably think that this corresponds to 1 billion amino acids to make all of the proteins right? Well it takes a lot more than that for it to work actually. So let us begin to describe how we go between these languages.

The origin of the genetic code is actually a huge problem that is glossed over. Indeed, DNA is only useful if is it translated, but the translation machinery is itself encoded in the DNA. This is a vicious circle—see Self-replicating Enzymes.

So let’s begin with the creation of RNA

If you mean from a primordial soup, then check out these chemical hurdles that must be jumped, and The RNA World: A Critique.

RNA Polymerase is what will form the RNA, but how exactly does it know to form it?

Actually it is a catalyst that joins high-energy derivatives of the nucleotides, the building blocks of the nucleic acids. For the high energy, ATP is required, and this is made by the world’s tiniest motor, ATP synthase.

Well it needs a promoter sequence that screams out “Hey come over here and copy this!”

Oh right, so just by chance, a protein evolved this amazing ability to be attracted to promoter sequences? Natural selection cannot explain it, because this presupposes a self-reproducing entity. One can’t use a self-reproducing entity to explain the origin of the first self-reproducing entity, obviously, and polymerases are essential for one.

and are usually found near the start point, but there are also enhancers/silencers that effect this process and found 1000’s of base pairs away!

And this system also evolved by chance?

To continue, RNA Polymerase will encapsulate a segment of DNA and move along it making base pairs to correspond to the DNA with he help of a bunch of proteins. So DNA contains a lot of promoter, enhancer, and silencer sequences that are not incorporated into the proteins and also do not have to be perfectly formed to truly function.

They require minimal complexity otherwise it won’t work at all!

Also, somewhere along the path of the formed RNA is a junk region, an Intron, that just gets snipped out of the sequence.

There is a lot more to it than the above implies. To form mRNA, it is necessary to remove introns and splice the exons together. This requires elaborate machinery called a spliceosome—an article in the journal Cell was entitled, ‘Mechanical devices of the spliceosome: motors, clocks, springs, and things’ [Staley, J.P. and Guthrie, C., Cell 92(3):315–26, 1998]. This is assembled on the intron, chops it out at the right place and joins the exons together. This must be in the right direction and place, because it makes a huge difference if the exon is joined even one letter off. Thus, partly formed splicing machinery would be harmful, so natural selection would work against it. 

This is yet another proof that the whole idea of junk DNA is junk science, as is increasingly being recognized:

Researchers the world over are confirming that non-coding DNA holds critical clues to a vast range of diseases; breast cancer, HIV, Crohn’s disease, Alzheimer’s, heart disease, ovarian and skin cancer … the list is growing daily. A leading figure in world genetics, Prof. John Mattick, recently claimed that, ‘the failure to recognise the implications of the non-coding DNA will go down as the biggest mistake in the history of molecular biology’ [Genius of Junk (DNA), Catalyst, Thursday, 10 July 2003].

So now we have a completed RNA for a protein, the thing with this is that while we prefer for this sequence to be correct and all, it doesn’t have to be perfect. If 3 codons wound up missing it doesn’t really cause much of a problem in general,

This can’t be serious, because 3 codons missing would mean that three amino acids would be lost from the protein, and this could be disastrous. It is not uncommon for a single amino acid in the wrong place to cause a serious malfunction, for example in the case of sickle cell anemia.

and if a wrong codon is present then it could still code for the same amino acid or one similar enough to code for a similar protein

And this is because our genetic code is optimal. There are millions of possible genetic codes where a mutation would be far more damaging. See The unity of life.

So now we have tRNA swoop in with an attached amino acid and connect along the mRNA and attaches all the amino acids together in a chain to make a protein in a process that I don’t want to get into right now.

Because this is most elaborate—the right amino acid is activated and linked in two steps to the right tRNA by aminoacyl-tRNA synthetases (aaRSs). These also have error-checking functions, including an ingenious double-sieve system.

Needless to say that all the amino acids are hooked up and then some modification occurs and the protein is folded.

Actually even the protein folding is most elaborate. It often needs a class of protein called chaperones which govern the folding of other proteins. This is yet another problem for chemical evolutionary theories—how did the first proteins fold correctly without chaperones, and since the chaperones themselves are complex proteins, how did they fold? See The Origin of Life: A Critique of Current Scientific Models (PDF file).

‘So now back to the original question: The evolutionist refutation of this that I have heard so far is that “it is incorrect” to assume that all the enzymes, little mechanisms etc must be functioning perfectly in order for the cell to live. But nobody that I have found has explained why this is so. I would like some one on here to elaborate, please.

So far from your understanding is that it is has to be correct…so let us educate you!

First there are large amounts of repetitive DNA sequences that don’t code for anything at all and aren’t a promoter/enhancer/silencer and don’t really affect you at all.

This is yesterday’s genetics. DNA has many more uses than coding for protein, as explained above.

Unique DNA is only 64% percent of the total.

Oh, so only about 2 billion base pairs to explain instead of 3? Or instead of about 1000 encyclopedia-sized books worth of information, just 600?

Next if you have an “error” in one sequence it probably isn’t detrimental, since it will most likely code for a similar protein.

Again, this is because our genetic code is optimal. But there are times when a single change between chemically very similar amino acids is harmful, which is why we have elaborate double-sieve enzymes to distinguish them.

Then there is the fact that multiple enzymes perform the same roles in the cell and the body and if one of these isn’t formed then it really doesn’t matter since you have other enzymes that fulfill the role.

Backup systems are a good design feature.

So, in most cases errors in the system aren’t as doom bringing as one might think, although in some very rare cases they can be.

Never mind the thousands of genetic diseases caused by mutations, in many cases of just a single base pair.

Even in your body there are probably a few copies of DNA with a mutation or two but,

A lot more, hundreds actually; but since we have our information in pairs, there is usually a backup copy.

there are enough proofreading factors to repair it all anyway.

And these proofreading factors are essential to avoid error catastrophe, yet according to evolution they must have arisen by time and chance.

To end a little math fun!

3 billion bases=1 billion codon language

64% of 1 billion codons is 640 million codons that are unique

640 million codon “symbols” that have 21 meanings, 19 amino acids, a 20th amino acid that means start, and a stop single.

Some organisms have special genetic codes that encode a 21^st or 22^nd amino acid.

So when you think of it as a 640 million codon text with just 21 “words” it doesn’t seem so complex does it?”

That is as silly as saying that a computer program can evolve without a programmer because it contains just two letters, 0 and 1. Because it’s not the letters but the arrangement that counts.

-Thats the end of it. When it’s broken down so simply, evolution seems to be more possible that way,

Even if this evolutionist were right that it were possible (and I have shown above he isn’t), that means nothing. A Christian should point out that we should not budge unless he can show conclusively that his view is the only possible one. This follows the advice of R.L. Dabney (1820–1898), Presbyterian minister, theologian and author, and Professor of Theology at Union Theological Seminary, Virginia, for over thirty years, had very sound advice on so-called ‘science’ vs the Bible. He was arguing against uniformitarian geology, but it applies to evolutionary biology as well:

The authority of the Bible, as our rule of faith, is demonstrated by its own separate and independent evidences, literary history, moral, internal, prophetical. It is found by the geologist in possession of the field, and he must assume the aggressive, and positively dislodge it from its position. The defender of the Bible need only stand on the defensive. That is, the geologist must not content himself with saying that his hypothesis, which is opposed to Bible teachings, is plausible, that it cannot be scientifically refuted, that it may adequately satisfy the requirements of all the physical phenomena to be accounted for. All this is naught, as a successful assault on us. We are not bound to retreat until he has constructed an absolutely exclusive demonstration of his hypothesis; until he has shown, by strict scientific proofs, not only that his hypothesis may be the true one, but that it alone can be the only true one; that it is impossible any other can exclude it [Discussions of Robert Lewis Dabney, vol. 3, Banner of Truth Trust, Carlisle, PA, p. 136, 1982].

I can’t seem to find any errors either, I was hoping that you may be able to help me regain my faith by showing me, as well as anyone else who reads this, the errors within, which I certainly hope there are.

I hope I have helped by more than answering specifics, but by showing how to think correctly about all scientific data.

In Jesus’ Name,
E.P.
USA

(Dr) Jonathan Sarfati
Brisbane, Australia

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