Mark: Are Mutations Random?

[swamidass (S. Joshua Swamidass)]

@Mark

Would you say he’s just using the wrong words to describe the process because he’s defining random incorrectly, or…?

Yes.

@Mark

Excerpt From: James A. Shapiro. “Evolution.” iBooks.

Wow. I’m fairly stunned to be reading this, realizing that it is from a scientist. It demonstrates basic misunderstanding of statistics. He is describing agreed upon science with idiosyncratic use of “random”.

@Mark

It is sometimes claimed that chromosome distribution at mitosis is random because there is no way to predict which of the two chromosome copies will end up in a particular daughter cell.

Notice that Shapiro agrees that this is true. He agrees there is no way to predict which of two chromosomes will end up in a particular daughter cell. This is a random “choice” or “variable” in the process. It is a maximum entropy decision, because it can go either way with equal likelihood. It is a single bit of randomness, one for each chromosome and each division.

@Mark

But the fact that one and only one chromosome copy goes to each daughter actually makes the process highly nonrandom.

No one disagrees with this too. There is an order to the randomness. There is a part that we cannot predict, and a part we can usually predict. These two things are true at the same time.

@Mark

If chromosome distribution were truly random, only 50% of cell divisions would produce progeny with a single copy of each duplicated chromosome in each daughter cell.

Now Shapiro starts to use random in an idiosyncratic way, making the claim that this process is not truly random. This is just a false. Instead, like all random processes, there randomness and order.

There maybe no such thing as randomness that has no order; that is a myth which might only appear possibly in quantum theory. The fact that there is order from one point of view, does not in any way erase the randomness we see from another point of view. As Shapiro defines it, there may be absolutely nothing that is “truly random”. This is a misleading abuse of terminology.

@Mark

Shapiro goes on to say that this takes place with 99 percent accuracy.

Which means it fails randomly, and is therefore not totally deterministic. I’m not sure I would take the 99% to the bank, but any uncertainty, then it is a random variable.

@Mark

How accurate does a process need to be in order to be considered non-random anymore? I know you have been saying it’s a matter of degree, but would it not sound a little silly to say that if something is 75 percent accurate, it’s 25 percent random? Maybe I’m thinking about this in a completely wrong manner.

It has to be 100% exactly to not be random. Depending on the precise thing we are modeling, very low probably events can be very important. There is a profound difference between a 0% likelihood event (deterministically impossible) and a nearly 0% likelihood event (very rare). The two are not exchangeable.

@Mark

I know you have been saying it’s a matter of degree, but would it not sound a little silly to say that if something is 75 percent accurate, it’s 25 percent random?

Absolutely not silly. This is precisely what we are quantifying all the time in information theory, statistics, and machine learning. We would say, perhaps, 75% explained variance, and 25% unexplained. 75% deterministic, and 25% random. 75% predicted and 25% random. There are several ways it can be said, but we are precisely measuring these things all the time. So of course it is not silly to describe what we are measuring.

@Mark

I’m assuming @Perry_Marshall will respond to you on his blog in a similar but more informed manner.

Not likely at this moment. He is not willing to engage on the forum. I’m not sure why.

[nwrickert (Neil Rickert)]

@swamidass

Now Shapiro starts to use random in an idiosyncratic way, making the claim that this process is not truly random.

He seems to be making a polemical point. And that’s unfortunate in a science book.

Here’s the real point, and this is for the benefit of @Mark : Just about everything in life is random. I put my foot on the brake pedal, and the amount of force that I use is random. This isn’t important as long as I stop the car in time.

I’m typing this on a computer, and we think of the computer as a strictly binary logic machine. But the signal generated by my key presses is random. It is random with a probability distribution, but there is randomness there. The computer is cleverly designed so that it operates properly in spite of there being some randomness there.

In what @Mark quoted, Shapiro is trying to make a dichotomy between “is random” and “isn’t random”. That’s just a mistake. The important dichotomy here is whether or not the randomness is important to our understanding of what is happening.

[Argon]

@mark, what Shapiro is talking about is flipping a coin and calling it ‘non-random’. You don’t know if the coin is going to land head or tails but it’s definitely going to land on a side. Cells have a very elaborate set of mechanisms to ensure each cell in a division has the necessary number of chromosones (excluding some specific cases like in blood cell development or meiosis). Cells get one or the other of the sets. This is, sorry to say, classic Shapiro-ism hyperbole and it is pretty much the reason why his particular ideas don’t tend to get a lot of traction among other knowledgeable scientists.

[swamidass (S. Joshua Swamidass)]

@Argon

This is, sorry to say, classic Shapiro-ism hyperbole and it is pretty much the reason why his particular ideas don’t tend to get a lot of traction among other knowledgeable scientists.

It is not merely that it doesn’t gain traction, it rightfully bothers many of us. This sort of claim is just frustrating careful attempt to engage the public to understand things like statistics and probability. By making a rhetorical objection not grounded in actual science, he just creating confusion.

[Argon]

I was trying to be a wee bit polite but…

He’s kinda like a Jeremy Rifkin…

[swamidass (S. Joshua Swamidass)]

Who is that?

[Argon]

Oh, you are young!

Rifkin was an early crusader/gadfly against recombinant DNA technology, circa 1970’s and early 1980’s. He often had the wrong facts but he was very certain of them. But still, reporters would go to him because they were trained to get ‘both sides of the story’. Some years later, at a scientific meeting, there was a roundtable of reporters discussing how they cover science and controversies. Asked about Rifkin, one science reporter said they were obliged to try to find other positions but that he personally tried very hard not to use Rifkin if someone better was available… Sadly, it looks like his Wikipedia article was well scrubbed of his recombinant DNA scare mongering period. Better to search ‘Rifkin recombinant DNA gadfly’. His book ‘Algeny’ was a howler of badly understood evolutionary biology.

[swamidass (S. Joshua Swamidass)]

@Mark

cognitive checkpoint control rather than mechanical precision ensures the reliability of eukaryotic cell division

Oh my. I did not even realize this the first read through. Whose “cognition” is guiding cell division? At the moment, all cognition of which we know eminates from minds in brains. Cells, however, do not have minds or brains. Is he arguing that God himself guides every division?

Shockingly, he denies a mechanical apparatus, of which we know exists, to ensure division correctly portions chromosomes. So we cannot even say that God is guiding it through natural means. Somehow Shapiro things a cognition is guiding chromosomes?

Can someone make sense of this for me? I had though he was just relabeling established science. This, however, seems to deep into something other than science.

[Argon]

@swamidass

Can someone make sense of this for me? I had though he was just relabeling established science. This, however, seems to deep into something other than science.

I think it’s ‘spin’.

[T_aquaticus]

@nwrickert

I suspect that part of the miscommunication here, is that some people thing of “random” as being opposed to “intelligent”. But they need not be. The owners of Las Vegas casinos are using randomness intelligently, and earning a pretty good income from that. You mention Noble’s term “harnessed stochasticity”. And that would be good expression for describing how casinos use randomness. And yes, biology can reasonably be said to also use “harnessed stochasticity”.

Continuing with that analogy, there is a pattern to the randomness in casino games. The example I often cite is the game of Craps where 7 is a much more likely outcome than 12 or 2. You get a Gaussian-type curve of results, with 7 in the middle and 2 and 12 on the edges of the distribution. That pattern doesn’t change the fact that the dice (if they aren’t loaded) aren’t influenced by the chips on the table. In other words, the dice are random with respect to the chips on the table. In the same way, mutations are random with respect to the fitness of the organism.

[nwrickert (Neil Rickert)]

@Argon

I think it’s ‘spin’.

Yes, that was my take.

[T_aquaticus]

I don’t know if this analogy will be helpful, but here it goes . . .

I think most of us would agree that the lottery is random, but what do we mean by that? What we mean is that the ping pong balls that are selected are unaffected by the ticket you are holding. Each ticket has a more-or-less equal chance of winning.

But is the lottery “truly” random? Using Shapiro’s misrepresentations of what random is, the lottery is not random. Here are a few examples:

The lottery drawings happen on set days on the calendar, such as every Wed and Fri. Since the drawings happen at predictable times Shapiro would argue that the lottery is not random.

When the lottery jackpot is higher people will buy more tickets which increases the chances of there being a winner. Shapiro would argue that the increase in rate of people buying tickets makes the lottery non-random.

Very rich people are less likely to buy lottery tickets than those in lower economic brackets. The distribution of ticket buying with respect to income would lead Shapiro to argue that the lottery is non-random.

The geographic distribution of ticket sales is not random. If you look at a map of the US you will see that some geographic areas sell way more tickets than others. The distribution of ticket sales would lead Shapiro to claim that the lottery is non-random.

With all that said, do you still think the lottery is random? I do. All of these other asides don’t take away from the central issue, that we can’t predict who will win. The ping pong balls are still completely independent of that ticket you are holding in your hand. The ping pong balls are not influenced by the wealth of the person holding the ticket, either.

The same applies to random mutations. The rate of mutations may change, different areas of the genome may be more susceptible to mutation, and mutations may produce certain patterns in a physical map of the genome, but they are still random with respect to fitness which is the measure biologists are actually focused on.

[swamidass (S. Joshua Swamidass)]

@T_aquaticus

they are still random with respect to fitness which is the measure biologists are actually focused on.

Careful, that is not precisely true if you mean not correlate with fitness. There is randomness with respect to fitness and order.

[T_aquaticus]

@swamidass

Careful, that is not precisely true if you mean not correlate with fitness. There is randomness with respect to fitness and order.

Using the lottery example, if there was some mechanism that caused a specific number to come up so that it matched a pre-determined ticket then it would be non-random. The fact that the range of ping pong ball numbers matches the range of numbers on the lottery tickets may be closer to what you are talking about. This would be equivalent to the increased rate of random mutations in immunoglobulin genes that you have cited before.

[Argon]

I really enjoy reading Arlin Stolzfus. He’s studied computational biology with W. Ford Doolittle and works in the areas of evolution, mutation and phyloinformatics. He’s also very knowledgeable about the history of evolutionary theory and the Modern Synthesis. Here is his review of Shapiro’s book.

I think Arlin has a good handle on where work on evolution is going today and has been very good at explaining where ideas still held by many in the field are likely incorrect. I particularly enjoyed his article here (Title: Why we don’t want another “Synthesis”).

[Mark]

The cognition should probably be put in quotation marks but Shapiro would wholeheartedly deny that it’s God who guides things. Rather, he would PROBABLY say it is cell intelligence itself.

[gbrooks9 (GeorgeB)]

@T_aquaticus

Continuing with that analogy, there is a pattern to the randomness in casino games. The example I often cite is the game of Craps where 7 is a much more likely outcome than 12 or 2

@T_aquaticus

And so it goes… over and over and over… any time i see the term randomness… i can count on you being in the middle of it.

Such a waste of time.

[Mark]

@swamidass,

It looks like you and Stephen Meyer agree on something! He accused Marshall on Unbelievable of “panpsychism.”

[T_aquaticus]

@gbrooks9

And so it goes… over and over and over… any time i see the term randomness… i can count on you being in the middle of it.

Such a waste of time.

Just for the record, when I first started researching the topic of random mutations years ago I was absolutely fascinated by the work that was done in the 1940’s and 50’s. Both the plate replica and fluctuation experiments were simple yet powerful in what they could show. They are perfect examples of brilliant scientists using simple concepts to solve really important puzzles.

So my interest in the topic started with biology, and is really limited to biology. I don’t have much interest in the wider philosophical or theological concepts.

[gbrooks9 (GeorgeB)]

@T_aquaticus

So my interest in the topic started with biology, and is really limited to biology. I don’t have much interest in the wider philosophical or theological concepts

@T_aquaticus

And that is why you are endlessly embroiled in a topic that distracts Christians from the mission of Peaceful Science.