This article is from
Creation 40(1):24–26, January 2018

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God’s DNA-detangling motors

The topoisomerase enzymes

by

detangling-motors

All living creatures contain incredible machines, as well as the ‘instruction manual’ to build them. This manual comprises sequences of chemical ‘letters’ (nucleotides) in the famous deoxyribonucleic acid (DNA) molecule, just as information in a book is written in letters on a page.

Furthermore, these instructions are copied to the next generation. You didn’t really get your mother’s eyes and father’s ears; rather, it was the instructions to re-manufacture your mother’s eyes and father’s ears that were copied to your DNA (see box below).

DNA’s physical dimensions pose many problems that would need to be solved before even the simplest life could function. The double helix is only about 2.5 nanometres (one ten-millionth of an inch) wide—too thin to be seen with any light microscope. (A complete turn of the helix is about 10.5 letters long.) But the whole DNA molecule is extremely long: the largest human chromosome, number 1, is composed of 220 million letters, and would be 85 mm (3.4 in) long if stretched out fully. If all the DNA in your cell were lined up, it would be about 2 m (6–7 feet) long! These enormously long, thin, sticky strands must be packed into a microscopic cell and then maintained without forming a mess of tangles and knots. The cell needs complex machines to do all this. These machines are amazing, complex, and a testimony to the genius of our Creator.

Unwinding the double helix

When DNA is decoded (that is, when the information is used to create a protein), the two strands of the double helix must be separated. And during reproduction, each strand is copied independently.

This requires special motors called DNA helicases. They are ring-shaped, with a hole for the DNA to pass through. But, since they are motors, they also need fuel. Helicases are powered by a ‘fuel’ called ATP, which is made by another motor, ATP-synthase.1 Using ATP as an energy source, a cyclic change in shape runs around the helicase ring at about 10,000 rpm—about the speed at which a jet engine turbine rotates. The helicase rapidly runs along the DNA and separates the two strands at the replication fork.2 Then, many other machines take care of decoding the DNA and putting the strands back together or copying the strands. This must run very fast, because the DNA copying speed is 1,000 letters per second and the helicase must stay ahead of the copying machines.

Supercoils

DNA’s helical (coiled) shape produces another problem that is amplified when helicase unwinds it to separate the strands. You can easily demonstrate the problem with a long multi-stranded rope: start in the middle and try to pull the strands apart. It will soon become too hard to unwind because of the resistance of the extra twists on both sides of the separation point. If you let go, the rope will tend to coil back upon itself—think also of the coiled cords on older telephones which too easily become tangled into coils upon coils. To compensate for every added twist in the forward direction, the DNA behind the unwinding site adds a twist, and also becomes supercoiled (overwound). In a cell, if the DNA were prevented from unwinding, then the cell could no longer make proteins or copy itself.

DNA-synthesis
DNA replication or DNA synthesis is the process of copying a double-stranded DNA molecule. This process is paramount to all life as we know it. Disclaimer: This is a simple diagram of a very intricate piece of machinery.

Detangling machines

The Creator solved this problem in living creatures with special protein machines (enzymes) called topoisomerases.3 They cut the DNA, rearrange it, and stick it back together. They must work ahead of the replication fork to keep the DNA from over-winding.

There are several classes of topoiso-merases, but they are grouped into two main types:

  • Type 1 topoisomerase cuts one of the DNA strands and temporarily bonds to both ends of the cut. Then the uncut strand is free to pass through the break. In either case, this relieves or ‘relaxes’ the strain, one twist at a time. Finally, the break is reconnected; this is called ligation.

    Type 1 topoisomerases don’t need ATP—the energy built up by the DNA’s over-winding is simply released, like a coiled spring when let go.

  • Type II topoisomerases are more complex. This type cuts both strands of the double helix and holds them apart. It then pulls a loop of the double helix from a non-cut section through the break. After that, the two strands are reconnected, the passed-through DNA is released, and finally the enzyme releases the reconnected DNA so the process can be repeated as necessary. This requires ATP for several of these steps.

    Type II topoisomerase is important for another reason: when DNA is replicated, sometimes the two ‘daughter’ DNA molecules can end up wound around each other like links in a chain, i.e. catenated (Latin catena = chain). Thus, separating these linked molecules is called decatenation, and this is a vital role of the type II topoisomerase.

Useless unless fully functional

These enzymes must do three things, otherwise they would be useless or even harmful: cut, move another strand through the cut, and reconnect. To show how important each step is, if any one step is disabled, the enzyme doesn’t work and the cell dies.

Indeed, some antibacterial and anti-cancer drugs work by targeting topoiso-merases. The class of antibiotics called fluoroquinolones (e.g. ciprofloxacin, levofloxacin) stops the reconnecting step of bacterial type II topoisomerase, leading to increasing breaks in the DNA, quickly killing the cell. Some anti-cancer drugs (e.g. camptothecin, topotecan) do the same thing to type I and type II topoisomerases in the cancer cells that were reproducing out of control.

Another class of drug called catalytic inhibitors prevents the ATP energy release and so works by stopping the first step of cutting. Instead of the cell dying by its DNA being ripped to pieces, the DNA just gets tangled up, so the cell can neither reproduce nor make proteins.

Problems for evolution

Clearly, random chemical reactions in pre-life conditions could not produce the first cell by small, gradual steps, each with a supposed advantage over the previous one and thus favoured by natural selection. Suppose this process produced an enzyme with the first step: cutting. Without putting it back together, this would harm the cell by chopping its information molecule to pieces!

But it’s even worse for evolution. Natural selection is by definition differential reproduction: that is, ‘A is fitter than creature B’ means ‘A has more surviving offspring than B.’ Therefore natural selection requires at least two self-replicating entities. This means that it can’t explain the origin of replication because you cannot reproduce until you have a way to replicate the DNA. And as we have seen, without topoisomerases, the DNA can’t be replicated because it would tangle up too quickly. Since natural selection can’t explain the origin of the first topoisomerase, Darwinian evolution cannot even get started.4

Still another problem is like the proverbial ‘which came first: the chicken or the egg?’5 That is: the instructions to build the topoisomerases are on the DNA, but these instructions can’t be read without topoisomerases to detangle the DNA. Even the simplest type II topoisomerase has 800 protein ‘letters’ (amino acids) split between two segments. It takes three DNA ‘letters’ to code for one protein letter, so the gene for this is about 2,400 letters long—too large to be read without detangling.

And these instructions couldn’t be passed on to the next generation without type II topoisomerases to decatenate the daughter DNA strands. Even the DNA of Mycoplasma genitalium, which has the smallest genome of any living organism, is far too large to decatenate on its own.

DNA: the best information storage system

DNA-storage-system

DNA is the most advanced information storage / retrieval / transmission system known. The information density in a living cell’s DNA is about 1,000 terabytes per cubic millimetre.1 So a living cell can store an enormous amount of information in a tiny space: the simplest living creature is an intracellular parasite called Mycoplasma, which has about 600 kilobytes of DNA, while each human cell has about 3 gigabytes.2

If all the information in each human cell were written in paper and ink, it would occupy about a thousand Bible-sized books (but only 200 times the size of the US tax code).3 But note that there is nothing in the chemistry of the ink that could produce the information in the books—they were not produced by pouring the ink on the pages! Rather, they were produced by an author arranging the ink into letters. In an exactly analogous way, there is nothing in the chemistry of the DNA ‘letters’ that would make them write the message of life.

  1. More details and documentation in Sarfati, J., DNA: the best information storage system, 9 October 2015; creation.com/dna-best. See also Batten, D., DNA repair mechanisms ‘shout’ creation, Creation 38(2):56, 2016; creation.com/dna-repair-shouts.
  2. For simplicity, I treat each DNA ‘letter’ as a ‘byte’ of information, which is ‘in the right ball park’. In reality, since there are four possibilities at each locus, we could use two bits to store each letter, which would reduce the overall memory requirement by 4-fold. But, using one letter per byte, we have 3.17 billion base pairs (bp), and two copies of the genome in each cell, so 6.34 billion bp, or 5.90 GB.
  3. Erb, K.E., [American] Tax code hits nearly 4 million words, Taxpayer Advocate calls it too complicated, forbes.com, 10 January 2013. For comparison, the KJV has almost 800,000 words.

Conclusion

Even the simplest living creatures need topoisomerases before they can read their DNA instructions to make proteins or pass them on to their offspring. These are complex, well designed machines that cut, move, then reconnect the DNA. Since reproduction is impossible without them, Darwinian evolution—random mutation + natural selection—could not have produced the first topoisomerases.

References and notes

  1. Thomas, B., ATP synthase: majestic molecular machine made by a mastermind, Creation 31(4):21–23, 2009;creation.com/atp-synthase. Return to text.
  2. A good description and video can be found in Unwinding the double helix: Meet DNA helicase,evolutionnews.org, 20 February 2013. Other fascinating videos can be found on DNA Learning Center,dnalc.org. Return to text.
  3. For more information, see DeWeese, J.E., DNA topoisomerases—the ‘relaxers’ and ‘unknotters’ of the genome, J. Creation 30(2):92–101, 2016. Dr Joe DeWeese of Lipscomb University, Nashville, Tennessee, has published many topoisomerase papers in leading secular science journals. See also the video Topoisomerase 1 and 2,youtube.com. Return to text.
  4. The proposed origin of life from non-living chemicals is commonly called chemical evolution. Return to text.
  5. The answer’s actually easy according to Scripture: God created the chicken on Day 5, which then laid the egg. Actually, to be precise, God made the galliform created kind that comprises heavy ground-living birds, which after the Ark diversified into chickens, partridges, pheasants, quail, turkeys, etc. Lightner, J., An initial estimate of avian ark kinds, Answers Research Journal 6:409–466, 2013 Return to text.

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Readers’ comments

King T.
Thank you for this wonderful article. It is one more weapon in the arsenal to use against the attacks and strongholds of the enemies of our God who is the creator of everything.
I intend to refer to this page for those atheists who want to pretend that life arising from non-living material is a trivial, hand waving exercise.
Roy L.
The tax code may be a poor example here because it may well have been just poured out of an ink bottle to randomly create unintelligible gobbledegook.
Michael B.
We haven't even been able to produce the proper "ink and paper" in the lab on which we might write such codes.
And even if all of that is there, the paper, the ink, the coded information, Who boots the process? Who says "Let there be life?"
Mike D.
What is so sad to me about evolutionist. If somehow mankind could design a computer program that could do all of this. It would be hailed as a great achievement by mankind & obvious to all it took Intelligent Design.

Funny thing is evolutionist claim this only "appears" designed. What blows that statement out of the water. This actual is FUNCTIONAL DESIGN not just design. Sure anyone could design something looking like it was designed when it wasn't functional despite still taking intelligence. Engineers do this all the time with failing designs until they get it perfected to where it Functions!

But the killing problem to evolution is all the design they see but refuse to acknowledge is FUNCTIONAL DESIGN! That is the death knell to their excuse. It's FUNCTIONAL not just " appearance". Our Engineer got it perfected so it was FUNCTIONAL DESIGN from the beginning!
Lawrence D.
I used to believe evolution because that is what I was raised on in the 50's and 60's. But then I studied science. That changed everything. Now I find myself almost daily saying, "God, you're a genius." (He knows my heart is worshiping Him.) This article is just another in a long string of articles and videos that affirm the genius of our Lord.

I recently saw a video with Dr. Joe Deweese about topoisomerase and was utterly amazed. This article goes even further.

Thank you for all the good work at CMI

Larry
Terry D P.
Re:
“Conclusion: Even the simplest living creatures need topoisomerases before they can read their DNA instructions to make proteins or pass them on to their offspring. These are complex, well designed machines that cut, move, then reconnect the DNA. Since reproduction is impossible without them, Darwinian evolution—random mutation + natural selection—could not have produced the first topoisomerases.”

Well said; the science underpinning this conclusion conforms with what God has told us in the Bible, about how he first constructed a fully formed dead man from the dust of the earth (without using Darwin’s evolution over millions of years), and then brought him to life:
Then the LORD God formed a [dead] man from the dust of the ground and breathed into his nostrils the breath of life [human spirit]. Thus the man became a living creature. — Genesis 2:7

Death occurs when God takes the human spirit from a living body.
Who committed the earth to his [God’s] keeping?
Who but he established the whole world?
If he [God] were to turn his thoughts inwards
and recall his life-giving spirit,
all that lives would perish on the instant,
and man return again to dust. Job 34:13–15

When God sends a human spirit back into a dead body, it will come back to life:
Moreover, if the Spirit of him who raised [Adam then Jesus] from the dead dwells within you, then the God who raised Christ Jesus from the dead will also give new life to your mortal bodies through his indwelling Spirit. — Romans 8:11
Dan M.
How anyone could understand the complexity and the information by which a cell functions and still believe in macro-evolution is as beyond my understanding as biological life itself! while people may disagree on who the creator is, they must deep down logically believe there is a creator or they are fooling themselves.
Did my laptop computer that I am using to type this message on spontaneously produce it self? Not a chance! It is too complicated, requiring thousands of intelligent thinking engineers to produce and my laptop is extremely rudimentary by comparison to the simplest cell.
Is there a creator? Absolutely! Would this creator communicate to us His existence? Yes, I believe so! In fact He came to save that which was lost (Matthew 18:11).
Father help this doubting world, that all may be saved.
Do you want to be with Him for eternity or be separate from him for eternity? The choice is yours!
WILLIAM M.
No sane, intelligent, informed person could possibly believe for a microsecond that this happened naturally. Not even given eternity and all the ingredients.

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