We’re Looking for a Few Good Mutations

Question from Nick:
How do you refute the argument that it is mathematically impossible for “good” mutations to occur and that evolution is mathematically impossible, and thus not a real theory, but a pseudoscience?

Short answer by SmartLX:
With evidence.

Okay, longer answer by SmartLX:
The idea that beneficial mutations are “mathematically” impossible is based on easily addressed misunderstandings of the process. The fact that the idea is so widely held by creationists despite being so easily addressed speaks to a common reluctance among their number to accept simple facts, if those facts are inconvenient.

A very simple counter to the claim is the fact that most individual mutations can potentially be reversed in subsequent generations. This is an observed and well-known phenomenon straightforwardly called reverse mutation. The list of reversible mutations includes many that would be regarded as “bad” or detrimental to survival and procreation. The reverse of these mutations would by definition be “good”, so there’s no barrier to this whatsoever.

The other effective counter is the set of beneficial mutations that have been observed. You can look them up on Google, or follow up on the short list given here. Most famously, the Lenski E.coli experiment tightly controlled an isolated population of E.coli and documented its acquisition, via repeatable mutation, of the ability to metabolise (eat) the citrate in its environment. The bacteria couldn’t do it, then they could. Creationists did everything they could to discredit this and failed pretty badly. We had our own little argument over it in the comments here (search the page for keyword “Lenski”).

Life, Oh Life, Ooohhh Liiiiife, Oh Life…(doo doo doo doo)

Question from Madnomas:
I just read your response to the question regarding biogenesis. While you gave the only answer you could have, it is severely lacking. To claim that it “is unlikely that the conditions could have been right at least once in the distant past” (paraphrasing) is a gross over reach. If abiogenesis were “not unlikely,” one would presumably be able to predict that the more we learn about the earliest life forms, the less complex these forms would appear, and the more likely the conditions that might be able to generate life would what we’ve found. However, it is exactly the opposite. Even the earliest life is infinitely complex. Not only is life extremely complex but has as its foundation, information. So, as we discover more about early life and the conditions surrounding the early atmosphere, it has only become more improbable, but without mutation and selection to fall back, we have to account for the appearance of information. So instead of casually brush off this extremely potent evidence for a creator, as understandably would for convenience, this is still a monumental challenge for atheism to address. Unfortunately, it’s only becoming more improbable with each new discovery.

Answer by SmartLX:
There is no physical or chemical barrier to an increase in the amount of information on Earth as long as we have the Sun, even before the emergence of life. I’ve explained this briefly here.

The first life was complex but it was less complex than much of modern life, unless you think human beings are no more complex than bacteria. And the Miller-Urey experiment gets a lot of flak but it proved beyond doubt that the introduction of electricity (via lightning) can produce amino acids, so inorganic processes do important work and therefore not all of the complexity had to pop up at once.

Not knowing how something happened is not an argument that it didn’t happen, except for an argument from ignorance. Eliminating every possible method might be evidence for same, but that clearly hasn’t happened as long as there are potentially viable models, and in this case there are lots. And the proposed alternative requires that we assume the presence and participation for an entity not only for which there is no evidence, but about which nothing is agreed upon even hypothetically. It would be much stronger to establish the existence of God without the requirement of faith and then argue that God created life than to support God with apparent creation.

Counting Chromosomes

Question from Ken:
I’m agnostic. There’s one thing I’ve always wanted to understand about evolution for a while, and I hope this is the place to get it answered.

When I learnt about it, in school and university, they expressed the idea of increment changes (whether modifications of traits that were already there, or new traits through mutation) over time, passed on through generations, “chosen” by the ability to procreate and pass on genes. That, I think I get for the most part.

But what I never really understood is how the number of chromosomes could change over time. How can chromosome numbers increase and decrease? I mean… let’s say an individual somehow has it happen, shouldn’t he or she be unable to produce viable (or fertile?) offspring with others of the species because of the wrong numbers of chromosomes? How does chromosome number change at all? The only way I know is through issues that happen in meiosis, the kind of stuff that causes Down’s Syndrome, and the XXY and X gender chromosomal abnormalities that cause problems in humans.

So, my question is: How can chromosome number change in to produce a viable, fertile individual for it to be able to spread to an entire species?

Answer by SmartLX:
It’s a good question because a sudden whole extra chromosome full of junk, or a whole one gone missing, can indeed cause serious defects. That said, it helps to remember that a chromosome is merely a container of genes, and the number of chromosomes has very little to do with the amount of genetic information in each.

The addition of a chromosome is the more complex process, so I’m linking to an explanation of one mechanism by PZ Myers. Essentially, one chromosome’s worth of genes ends up being shared by two, and at first it can interact just fine with the old combined chromosome because the total sequence is the same. This does introduce a higher rate of error until individuals with the split chromosome start mating with each other, at which point there’s no longer a downside. Once the new number of chromosomes is settled, each chromosome is free to mutate independently and add new genetic information in the usual ways.

As for a reduction in chromosomes, we need look no further than our own genome. Our #2 chromosome pair is equivalent to two separate chromosome pairs in our closest ape relatives, but fused together. You can tell because there are two end markers (telomeres) right in the middle of it. No genetic information was lost, it was merely repackaged. This, importantly, is a very clear example of the kind of predictions one is able to make using evolutionary theory: the number of chromosomes in our genome compared to our ancestors’ (i.e. one less) tells us that exactly one fusion must have occurred, and we can then check the genome for only one extra set of markers.

The Very Obvious Decline of Religion

Question from Adam:
Hi again,

What is up man? I am writing today to bring up something that I am very interested in. I know you are not in the U.S….but I am so I will be talking from that perspective.

I have this theory that with the global phenomena of the internet, religion will start to fade away. I think that kids growing up with access to whatever knowledge they want will have major perspective compared to people in the past who only knew what their family/church/or community told them. I understand that indoctrination to children will not stop, but I think at some point soon, the kids of today will become the adults of tomorrow, and even if they still hold onto some beliefs from their indoctrination, they will be less likely to force those beliefs onto their kids (because of their gained perspective).

I think kids these days are gathering random knowledge from the internet more than ever before. This gives them more tools to form their own informed belief, rather than just taking what they are told.

I think the first thing we will see is a large increase in the number of “spiritual” people who believe in some magics, but think major organized religion is ritualistic bull for the most part. I think once these spiritual folk have kids, we will have a real coming of atheists (or at least non-spiritual agnostics).

Since monotheism largely destroyed polytheism, it has held a strong grasp onto the people of the world. Nothing has been able to touch monotheism since! I think the internet might be the first real threat to it. I really believe that being able to see different religions, different cultures, and more openly know what your friends are can break a child from the cycle. I think people are slowly breaking away from “I’m Christian because I was raised Christian”. And I think it is exciting!

In the U.S. there have been polls or whatnot of atheism growing. The whole “nones” thing. I even saw a prediction that in 40 or 50 years most of the U.S. might be in this group. I am going to try to be optimistic about this!

I hope this mind trap will largely die out with the 40+ population in 40 or 50 years. I want to see progress. I would love to know the majority of this world isn’t latching onto hopes of magic, and beliefs of incredible stories from poorly written books.

What do you think about the future of the U.S.? Or of the world? Will we make it out? Gosh I’d love to make a series or movie about this. “The end of religion”.

Answer by SmartLX:
Well, you’re “predicting” some things that have already happened. The “nones” directly represent an increase in the number of “spiritual” people as opposed to “religious” people as much as they represent a rise in the number of atheists. The United States are an outlier when it comes to adherence to religion in developed countries; there are some countries in Europe where they’re already asking whether religion is effectively dead. The internet stops any religion from completely suppressing information contrary to its dogma, even savvy religions like Scientology which installs a filter on its members’ computers. In places where particular religions are increasing, for instance Africa and China, they are doing so by cannibalising the followers of either archaic tribal religions or pseudo-religions such as the communist worldview. Proselytisers can’t make a statistically significant dent in the free atheist demographic, and many of them know it.

I wouldn’t hazard a guess when or even whether religion will die out completely, but I see no reason why the trend of deconversion and secularisation won’t continue for the time being. It’s not just atheists who have this outlook, as an unknown youth pastor’s Facebook status recently revealed:

“Information and time are on the side of nonbelievers. Every single day that the idea of a god persists, more will disbelieve in His existence. There is simply nothing we can do about it but accept the inevitable and hope they do not treat Christians the way Christians have treated them.”

Why isn’t evolution completely impossible?

Question from Abdul:
How can a undirected process create DNA that is way more complex than Microsoft or a quantum computer?

Simplicity cannot create complexity.

I don’t get Darwinian evolution, can you guys please help me out.

Answer by SmartLX:
Abdul, I thank you for correctly referring to evolution as an undirected process. Many who challenge it make a point of calling it a random process, which it certainly is not.

Complexity can indeed emerge from simplicity. The laws of the universe allow order and information to increase in a given area, usually with the help of an influx of energy. Otherwise there would be no increases in complexity at all, even with intelligent assistance; buildings could not be erected, coherent thoughts could not be assembled and ink could not be arranged to form words. Practically nothing we do would be possible, and physics wouldn’t be able to explain anything at all.

If an increase in order and complexity is physically possible, then how does it happen without guidance? It can definitely happen by chance, such as when the letters in alphabet soup float into the order of a word or a name, but just as often it happens by deterministic physical mechanisms doing their own thing. Evolution gets its raw material from mutations, which can duplicate genes in a sequence or recombine them in many different ways.

Once the mutations have happened, some life forms have the mutation and some don’t. If the mutation has any effect, positive or negative, on the likelihood that a life form will survive and procreate, then over multiple generations the proportions of the population with and without the mutation will change. Over thousands of generations, mutations upon mutations can have profound effects on the nature of the life forms. Life has had about 3 billion years to compound this effect and produce the immense biological diversity we see today.

If there really were a saying as simple as “simplicity cannot create complexity” that immediately disproved Darwin’s theory of evolution, it would not have survived for 150 years. Most scientists barely have the resources to do their own research, let alone sustain a massive worldwide conspiracy to pretend that a bogus theory is valid. Why would they do that anyway? It’s a terrible way to promote atheism, for example, because many scientists are still religious and many religious people accept evolution. No, the theory has survived as a scientific theory because it has enormous explanatory power, requires very few assumptions and is backed by a mountain of evidence.

DNA and Information

Question from Koalanu:
If the DNA structure is simply an illusion, is it possible for the monkey theorem to be true?

Could this also mean that the structure of reason, creativity, and emotion – could these all be illusions within our head?

Can we compare the complexity of DNA and Microsoft together?

Thank you guys soo much, I’ve been tryna look for an answer, but these questions have been bugging me a lot.

Answer by SmartLX:
The structure of DNA is not an illusion, unless you get all philosophical and suppose that the whole world could be an illusion. DNA is as real as anything else, and it’s really arranged in spiralling combinations of the four basic components: adenine, cytosine, guanine and thymine or A, C, G and T.

For DNA to allow for the monkey theorem, by which I reckon you mean the theory of evolution, it only has to do one thing: produce copies of itself, either directly or by the roundabout route of building a life form which then produces more DNA. It also has to do this imperfectly, so that the copies are not exactly the same as the original. (If it worked perfectly, there would be little or no change between generations.) Fortunately, this is exactly what DNA does, so the process of natural selection has all the raw material it needs.

Reasoning, creativity and emotion are products of the bio-electrical activity in our brains. We can be pretty sure of this because they can all be crippled if your brain is physically damaged. This doesn’t mean they’re illusions; it just means that we have abstract representations of the information we all process, because it’s easier to think that way.

DNA contains information of a very specific kind, namely strings of chemicals represented as, for example, ATCGGCGGTACTATCA. Microsoft products run on computers which store information as a series of bits, for example 0100100101010111. Both of these simple forms of information can, with a long enough series, represent just about anything. The difference is that the information in DNA has arisen naturally over a very long time, while most of the information at Microsoft was directly programmed in, or else generated by deliberately designed programs, very recently. (The rest is the result of data corruption.)

Hope that helps.

DNA and Intelligent Design

Question from John:
Can you believe in ID and Evolution? If not how can we prove that a undirected process created information and design within DNA? And if it was created by a misguided process does that mean that everything around us is simply a delusion?

Answer by SmartLX:
Many people, including some scientists and even biologists, believe that evolution happened but God or some other “designer” guided important parts of it, the main instance being the development of human beings. This position is known as theistic evolutionism. It’s not normally called “intelligent design” because self-proclaimed ID proponents like those in the Discovery Institute oppose undirected evolution explicitly; their goal is to establish their designer as necessary to the process, not just a possible part of it.

Undirected processes create additional information within DNA all the time through mutation, often under observation. The easiest-to-understand mechanism by which this happens is gene duplication: a small part of a genome is duplicated, changing the instructions it gives the same way an extra “o” changes “hot” to “hoot”. Here’s a video by Don Exodus which goes into more depth; I’m sure you can find many more.

By definition, an undirected process cannot create true design, which implies the existence of a designer. An undirected process can however create the appearance of design if a selection process exists which favours more elegant solutions to physical challenges, and that’s exactly what natural selection does. Even Richard Dawkins often says that living things look designed; this has no bearing on whether they really are.

Everything we sense around us might well be a badly distorted image of what’s really there, or even a complete hallucination, but we are able to test our surroundings and find consistency. When we let go of a ball, it always falls down (unless we’re underwater). When we feel something hot, it hurts us to touch it. We know from smell alone whether someone’s farted in our elevator. The world we see gives every impression of being a real, tangible world, even if we might not be seeing it as it truly is. Nobody said evolution produced perfect results, but it’s given us good enough senses to make some internal sense of the world and survive in it. That’s technically all we need.

The Atheist’s Riddle

“Perry Marshall presents himself as an invincible defender of his supposed proof of an Intelligent Designer, standing atop a mountain of vanquished counter-arguments from hordes of atheists.”

Argument taken directly from Cosmic Fingerprints:
1) DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism.
2) All codes are created by a conscious mind; there is no natural process known to science that creates coded information.
3) Therefore DNA was designed by a mind.

Answer:
Perry Marshall presents himself as an invincible defender of his supposed proof of an Intelligent Designer, standing atop a mountain of vanquished counter-arguments from hordes of atheists.

The plain logical error in the argument is in the second premise, and it’s the one logical fallacy I come across more than any other: an argument from ignorance. “There is no natural process known to science that creates coded information.” That’s not the same as saying there really is no such natural process (which would be a simple unsupported statement rather than a fallacy), but it expects us to assume as much. Is Mr Marshall, or any human alive, familiar with “all codes” in the universe? What qualifies anyone to make such a sweeping statement? This attempted proof by elimination of the origin of DNA must leave room for unknown alternatives to maintain any honesty, and is therefore not a real proof.

I realise that the fact of the logical error is not such a brilliant counter-argument when you’re actually trying to convince people. There are plenty more objections, and Marshall has posted and replied to many on his site. He hasn’t always done so convincingly, though you can judge that for yourself. I’ll just take one approach as an exercise.

As support for the argument that all codes are designed by a mind, Marshall argues that random processes do not produce information. (I’ve been through this at length, years ago.) His primary demonstration is his own text-based random mutation generator which takes a sentence and, through single-letter changes, turns it to nonsense.

Marshall admits that the mutation utility does not simulate natural selection, the non-random element of evolution. Furthermore, he’s not interested in adding that functionality to test his own argument. (He says instead that the reader is free to do it for him. Several people have, beginning thirty years ago with Richard Dawkins’ “Methinks it is like a weasel” program and continuing with browser-friendly programs like Mutate.)

He argues that natural selection would only create sensible sentences if words only mutated into other meaningful words, but that’s not applying natural selection at the letter level. An ideal extension of his program would present several choices of mutation at each step, and allow those letter mutations which destroy the legibility of a word to be manually or automatically ruled out. (The real world equivalent is a serious birth defect, which would keep a creature from breeding or even living long enough to breed.) In Marshall’s program, detrimental mutations are allowed to compound until all sense is lost. Of course we won’t likely get anything useful out of it.

Forgetting even the mechanism of natural selection, I submit a basic argument for the possibility of chance creating information which I’ve used before: think of a large grid of squares which can be either black or white, but all start as white. If you randomly pick the colour of every square at once, there is a chance, however small, that the newly black squares will form a simple but clear picture of a rectangle, or the letter G, or Elvis. Without adding any extra material, chance can increase the amount of information the grid provides. The prebiotic chemicals only had to manage a feat like this once, given potentially unlimited opportunities, to come up with DNA or its precursors.

SmartLX