Defining Evolution 17: Molecular Clocks

There was a very popular song when I was younger which expressed the theme, “Everybody’s Working for the Weekend.” While there is something to be said for the Friday night whistle before the two days reprieve from the fluorescently lit daily grind, there is something even more special about Thursday nights, and that something is Nachos. Every Thursday I meet my friends Bill, Carl, Tom, and Captain Blue Beard at Danny’s Bar, Grill, and House of Rabblerousing for friendship, food, and mutual sharpening of the old wit. Nothing keeps the old gray matter jogging uphill like friends with keen minds pursuing some matter of debate together. Of course, experience tells us that the gray matter takes a bit of a break once the oxygen is diverted from the head and into the great quantities of Nacho which will be consumed. As soon as we have our frosty mugs of root beer, the clock is ticking.NACHOS logo

On this particular Thursday night that metaphor was apt as our good friend Carl had once again come prepared to defend his consistent assertion that Evolution is supported by “Mountains of Evidence.” As far as I could tell, we had well and good swept his mountain into a molehill, but Carl was nothing if not tenacious. He was the intellectual equivalent of a bought with the flu, but I digress.

When I took my seat and had enjoyed my first taste of root beer, I noticed on Carl’s face the smug look of superiority which told me that I was about to be treated with an education from some fountain of knowledge, such as Wikipedia. “What, ho, Carl?” I said. “Something on your mind?”

“I did a little homework,” Carl replied, “in order to help you poor religious zealots to overcome your scientific deficiencies.”

“Do tell!” I said with almost sincere enthusiasm.

“The modern study of genetics,” he continued, “has opened up new worlds of information which have continued to provide solid evidence for Darwinian Evolution.”

“Well, that’s funny!” exclaimed Blue Beard. “I thought we dealt with the ‘solid evidence’ when we looked at the fossil record!” Blue Beard laughed at his own pun. “But as I recall, that didn’t work too well for Darwin there, did it, lad? It seems to me that instead of providing mountains of evidence, Darwin was literally failed by the evidence in the mountains!” Once again Blue Beard laughed at his own pun, and then washed it down with some root beer.

“As I was saying,” continued Carl, never one to be derailed by information he disliked, “the study of genetics has provided more scientific evidence for evolution. Just as one example, molecular clocks have provided undeniable proof for common evolutionary ancestries and ongoing evolutionary change.”

“I think if we’ve proven anything,” I suggested, “it’s that there is no such thing as undeniable proof. But I digress. I suppose we need to ask what a molecular clock is.”

“I thought you might,” said Carl, pulling his notes out of his briefcase. He read to us the following:

“The molecular clock is a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins.

https://en.wikipedia.org/wiki/Molecular_clock

“Wikipedia,” I noted. “How unexpected.”

“There’s nothing wrong with Wikipedia,” said Carl.

“Of course not,” I replied half-heartedly. “But I still think you might help us understand this molecular clock business. I don’t think the Wiki has made it clear as crystal for me.”

“It’s very simple,” said Carl in his best scholarly tone. “We can use genetic and molecular studies to determine when related species branched off of their common ancestor.”

“Clear as mud,” noted Blue Beard.

“Maybe an example would help,” suggested Tom.

“Yes,” said Carl. “Of course. Well, we know that humans and chimps branched off of their most recent evolutionary ancestor about five million years ago. We also know from genetic studies that chimps and humans are about 98% similar in our DNA, which means we can prove that our evolutionary changes have been happening at a rate of one percent of our DNA every two and a half million years.”

“And this proves, what again?” asked Bill.

“It proves,” said Carl in that tone he gets just before I explain to him what he’s actually said, “that chimps and humans had a common ancestor five million years ago, and we’ve been acquiring genetic changes via mutations at a rate of one percent of our genome every two and a half million years.”

“So let me get this right,” I said in that tone I get just before I explain to Carl what he’s actually just said. “We’re going to use the rate we can’t measure of a process we never observe to determine how long ago something we didn’t observe happened.” The light of understanding began to flicker in the eyes of my friends, causing each a slightly different mental and emotional journey.

“Sometimes,” I added, “when you describe something accurately, it sounds like you are being sarcastic when you are not. This is one of those times.”

“You obviously just don’t understand,” said Carl. “Maybe this will help. Here’s a quote from http://www.evolution.berkeley.edu/evosite/evo101/IIE1cMolecularclocks.shtml.”

Over the course of millions of years, mutations may build up in any given stretch of DNA at a reliable rate. For example, the gene that codes for the protein alpha-globin (a component of hemoglobin) experiences base changes at a rate of .56 changes per base pair per billion years.

“Who’s been tracking the mutations in that gene for billions of years?” asked Blue Beard.

“No one, obviously,” replied Carl. “We can figure these things out by examining evidence left over from earlier stages in earth’s evolutionary history.”

“How that?” asked Blue Beard.

“Well, I’m sure they compared DNA from ancient life to today’s,” said Carl, losing steam.

“The half life of DNA is just over 520 years,” said Bill. “That means in seven million years every single bond is broken and the DNA is no more.”

“How old are those dinosaurs again?” asked Blue Beard. “About ten times that, according to you, eh Carl? But still, no BILLION year old DNA lying around to test eh?”

“Look,” said Carl, clearly dissatisfied with the direction the conversation had taken, “I don’t know exactly how they figured it out, but they did.”

“I’m sorry, Carl,” said Tom. “I still don’t understand the significance of this.”

“Molecular clocks tell us how regularly mutations happen,” explained Carl. “These guys have been trying to argue that evolution by genetic mutations is impossible because of how complex DNA is and all of that, but these molecular clocks show how probable it is since, say in this chimp and human example, we only need the DNA to acquire a one percent change in their genome every two and a half million years.”

“Say, Tom,” I said, “you’re good at math. How about you help Carl here show us how easy this is for evolution to accomplish?” Tom and Carl both looked confused, but Tom agreed to be of service. “Carl, tell Tom here how many nucleotide base pairs humans have.”

“We have about three billion,” he said.

“And you said that chimps and humans have genomes which are a mere, what, 2% different?”

“Hang on,” interjected Blue Beard. “How do you figure that? Is that true?”

“It’s not even close to true,” I said. “And it is a very funny story over all, but for right now let’s just assume it is true and continue the story as if it were.” Blue Beard agreed and Carl got that look that tells me he’s starting to think I’m up to something. I would think that by now I was getting rather predictable, but Carl doesn’t like to get bogged down in the details. “So, we have three billion base pairs, which are, over all, only two percent different than chimps, meaning a change of… Tom, what is two percent of three billion?”

“Two percent of three billion is sixty million,” said Tom.

“And sixty million changes over five million years is how many per year?”

“Twelve changes per year.”

“That’s nothing!” exclaimed Carl.

“But humans and chimps don’t reproduce every year,” I reminded us. “So, let’s say it’s every fifteen years.”

“That’s 180 mutations per generation,” said Tom. “Assuming this whole thing is regular, you know. Like Clockwork.”

“That’s the idea!” said Carl. “And look how easy it is to collect these simple mutations!”

“And this is where I remind us,” I said, “that we know of almost 400 places in the genes that make blood cells where as little as ONE nucleotide change can destroy us.”

“You’re just trying to change the subject,” huffed Carl.

“The subject is the rate of mutations,” I reminded him. “But mutations are far more likely to be lethal than helpful. Even if we assume everything you’ve said here about our DNA mutating by 180 nucleotides per generation, you have only stumbled upon a new and scary feature of modern genetics- genetic entropy.”

“What’s that?” asked Tom.

“Genetic entropy,” said Bill, filling in the medical gaps for me, “is what we call it when neutral mutations build up over time until they become lethal. They are like tar in your lungs. The amount from your first cigarette probably won’t kill you, but over time the tar builds up until your insides resemble a fresh parking lot.”

“If that was true, then we’d all have gone extinct millions of years ago!” insisted Carl.

“Funny you should say that,” I said, again searching into my personal computation device. “Because that’s the questions a lot of people are asking. Even in the title of this article, the problem is acknowledged:

“Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?” by Alexey Kondrashov, Journal of Theoretical Biology 175:583–594, 1995.

(Sited in http://creation.com/time-no-friend-of-evolution)

“So when you study this molecular clock,” I continued, “and see how fast mutations are accumulating, you find that those mutations are harmful. They cause things like cancer and birth defects. The conclusion is that we can NOT have been on the planet for a hundred thousand years, or we’d have gone extinct already.”

“But if all these mutations are doing is killing things,” said Tom, “then why are people claiming the molecular clock to be evidence of evolution?”

“It’s because they are assuming evolution to be true and then wedging the data into that model, just as they do with the fossils.”

“You’re just begging the question!” exclaimed Carl. “You’re only rejecting the conclusion because you reject evolution, so you’re guilty of the same logical fallacy you’re trying to accuse me of!”

“A mind like a steel trap!” added Blue Beard with a smile. “Let’s think about the facts of the case for a moment without any presumptions,” he said. “Genetic studies tell us two things. First, that mutations happen regularly enough that every generation gets more than a hundred changes to their DNA. Second, that as little as ONE change can kill us. Now, Carl, which conclusion do the facts lead to? Evolution over millions of generations accidentally writing thousands of new genes, or the idea that our species was made six thousand years ago with a perfect genome which has been breaking down over time?”

Carl refused to answer. I optimistically try to take this as a good sign.

“There is one more thing,” added Bill. “Genetic studies don’t show one to two hundred mutations per generation. It’s actually much more than that. Either way, genetics are the Achilles heel of deep time.”

“The conclusion seems obvious,” I said, “but there’s an even bigger objection to this molecular clock business. Stasis.”

“What’s stasis?” asked Tom.

“Stasis is what we call it when things don’t change for long periods of time. Now, as you know, I don’t buy the deep time dates, but let’s assume them to be true for a minute. You know what a horseshoe crab is?” Tom nodded, so I continued. “Well, according to the fossil record, and the evolutionary assumptions that go with it, those guys have been on earth for five hundred million years.”

“Five hundred million years?” echoed Tom with surprise. “That’s a long time.”

“And the point is,” I clarified, “if you assume the molecular clock to be legitimate, meaning that DNA is changing every generation with regularity, then how do you explain a species remaining unchanged for hundreds of millions of years? But if you can claim a species HAS remained unchanged for five hundred million years, how can you possibly claim that DNA is evolving at a predictable and constant rate?”

“There goes all the wind out of your sails, eh Carl?” added Blue Beard. “If stasis can keep some creatures like the coelacanth and the horseshoe crab the same for hundreds of millions of years, then of what value is that “molecular clock” you’re arguing for? If mutations happen so regularly that they can be used as a clock, then stasis should not be happening at all, let alone for so many species for such vast amounts of time.”

“Yet, stasis is not rare,” I said. I read the following quote:

Fossil bacteria dated 3.55 billion years “…look identical to bacteria still on Earth today.”

-Peter D. Ward, Donald Brownlee, Rare Earth, Why Complex Life is Uncommon in the Universe, 2000, p. 57.

“If something can remain unchanged for 3.55 BILLION years,” I said, “then there might be less to this evolution thing that the brochure lead us to believe.”

“Oh, now, if we’re quote mining,” said Bill, “then I have something to add. Listen to this.”

It is often convenient for evolutionary biologists to assume that certain proteins evolve at a fixed rate. Such proteins can be used as “molecular clocks,” since one can use them to estimate when species diverged. However, these clocks sometimes behave in an erratic manner which calls into question their use and even the entire theory of evolution.

http://www.cs.unc.edu/~plaisted/ce/clock.html

“And here’s another which says something similar.”

Even supporters of the rate constancy hypothesis acknowledge the fact that molecular clocks can, in fact, behave erratically. Some genes have been shown to evolve at disparate rates across genes and lineages and over time (Ayala et al.1998). A great deal of data exists that shows this variation.

http://www.as.wvu.edu/~kgarbutt/QuantGen/Gen535Papers2/Molecular_Clocks.htm

“Would it be all right,” asked Blue Beard, “if I quote from a creationist source?” Carl immediately said “no,” but the rest of us gave him the nod of affirmation, so he read us the following:

Despite the fact that the genetic clock data are clearly manipulated to conform to vast amounts of evolutionary time, the results rarely support the overall evolutionary story. In fact, the following problems are often encountered.

  1. Different genes give widely different evolutionary rates.
  2. Different types of organisms exhibit different rates for the same type of gene sequences.
  3. Genetic-clock dates that describe when these creatures supposedly split off to form new creatures (called divergence) commonly disagree with paleontology’s timescale despite being calibrated by it.1

http://www.icr.org/article/9002

“I’ve got one as well,” I said, and read the following.

Perhaps the most remarkable data supporting a young creation were recently published by a large group of secular scientists who are involved with mapping DNA variation across the entire human genome.26 This massive effort has just produced a huge dataset that the researchers call “a global reference for human genetic variation.” In their report, they state:

Analysis of shared haplotype lengths around f2 variants suggests a median common ancestor ~296 generations ago (7,410 to 8,892 years ago), although those confined within a population tend to be younger, with a shared common ancestor ~143 generations ago (3,570 to 4,284 years ago).26
(
The 1000 Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature. 526 (7571): 68-74.)

http://www.icr.org/article/9002

“That sounds like they’re saying,” said Tom analytically, “that all humans have a common ancestor somewhere between 9,000 and 4,000 years ago.”

“Almost,” I said. “They’re saying that these genetic studies show a common human ancestor- Adam and Eve- between 7 and 9 thousand years ago.”

“There goes your six thousand years!” said Carl.

“It’s a lot closer to my six thousand than to your hundred thousand,” I reminded him. “But this quote is also saying that, for any one population, they had a common ancestor about three and a half to four thousand years ago, which would have been at the Tower of Babel dispersion event from Genesis chapter eleven.”

“So what?” said Carl. “What does that prove? It still shows the human race too old for your Bible stories.”

“I have another quote which clarifies it a bit,” I said, reading the following.

The review in Science’s ‘Research News’ goes still further about Eve’s date, saying that ‘using the new clock, she would be a mere 6000 years old.’

http://creation.com/a-shrinking-date-for-eve

“So you’re saying,” said Tom, “that this molecular clock business has been used to prove that, the first female human lived 6,000 years ago?”

“How about that!” exclaimed Blue Beard. “Isn’t that exactly what the Bible says? Well now Carl, there might be something to this genetic clocks business after all!”

Carl had no comment, and it was just as well as out Nachos soon filled the silence that followed Blue Beard’s comment with the heavenly sound of crunching chips covered in everything good. The clock had run down on our science fisticuffs, but I had a feeling that another bought might be waiting on Thursday next.

Happy Nachos! And thanks for letting me be your Rent-A-Friend.

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