Category Archives: History

The speed of evolution – revisited…

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I have been keeping my eye on the evidence that ‘life experience’ can be passed on in your genes.DNA

It has been proposed many times as a mechanism of evolution, and indeed was considered likely before the concept of ‘selection’ was understood. It’s attractive because saying that ‘survival’ is the one and only way to adding value to the genes seems, well, wasteful.

Surely, you’d think that a fear of snakes based purely on the idea that people who were not afraid of snakes were ‘taken out’ of the gene pool by snakes, is less efficient than a mechanism that captures experience – that snake killed my dog, I should avoid snakes, and so should my kids…

However, once DNA was understood and shown to be dense with what seemed to be all information that could ever be needed, dissent waned to an all time low. The mechanisms of DNA were pretty clear – your DNA was set at birth and while it might mutate a little randomly, had no way to ‘learn’ from your life before being combined with a partner’s to create offspring. The case seemed pretty settled.

There remained niggles though. I worried about the speed of evolution as we have so very much to learn and so little time to evolve! So I looked for ways evolution could amp up its power. It seemed to me that nature, so darn clever at self-optimisation would make improvements to our design based on non-fatal experience, or indeed passive observation.

Others similarly concerned continued, often in the face of deep scepticism, to study what is called epigenetics, the science of heritance not coded by DNA – and thus having the potential to be edited during our lives.

I first heard about it around 10 years ago when media reported that the actual DNA sequence was not the only way info could be stored in cells – in theory the histones present can affect how the DNA ‘works’ (how genes are ‘expressed’) and their presence could thus change the characteristics of any lifeform coded therein. The type and number of histones may be few (relative to the number of base pairs in DNA) however, the many locations and orientations they can take create a fair number of possible combinations and permutations.

When I heard about this theory, I was put into a state of high curiosity. On the one hand, it was a little blasphemous, but on the other hand tantalising. If nature could find a way to combine the power of selection with the potential benefits of life experience, we could get much faster and more effective evolution.

My curiosity was soon rewarded with another possible mechanism for smuggling info to the next generation. DNA methylation – the idea is that DNA can host little ‘attachments’ in certain places. These may be temporary, and reversible, but they have now been clearly shown to alter how the DNA expresses itself.

On the face of it, the evidence that DNA expression is environment dependent is rather strong, but the idea that the environment around the DNA coil actually contains consistent and persistent intelligence picked up during our lives is much harder to prove.

And so teams have been beavering away trying to get to the bottom of this, and this week one such group has fresh news for us. A Nature Neuroscience paper has tested the theory in a rather clever way.

lab miceThey started by teaching some mice a new fact (that a certain smell would be associated with trauma) and then later, tested their kids. Lo and behold the kids whose parents had been taught fared significantly better in the test than untrained, unrelated mice.

This may sound a little trivial, but you must remember that the current ‘popular’ understanding of genes is that they only gain intelligence by surviving – or more precisely they shed stupidity by dying. However, here we are seeing information pass between generations without the need for anyone to die.

Furthermore, because of the carefully selected lesson taught to these mice, the researchers were actually able to see that a specific part of the DNA, while not different in design was nevertheless more active.

Now, I do not know enough about DNA to double-check this claim, but you can rest assured others will – because that’s what journals are for – and in this case the implications are huge.

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Like what, you ask?

Well, off the top of my head, it means that much of what we do between birth and reproduction will affect all our descendents – this undermines the idea that one’s body is one’s own to do with as one pleases.

It also indicates that there is potential for us to deliberately control the expression of our DNA, allowing us to do some genetic engineering without actually changing the DNA sequence.

More importantly, and more controversially, it would mean natural selection would not need to explain all the marvellous diversity we see around us on its own.

It remains to be seen what proportion of our ‘design’ is coded for outside the DNA, or indeed how much this mechanism can improve or speed up evolution, however I for one hope it works out to be right and that mother nature has indeed figured out how to seriously boost the power of selection.

What exactly is ‘science’?

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I used to think science was the practice of the scientific method; i.e. you propose a hypothesis, you develop a test of the hypothesis, execute it and prove the hypothesis.

That worked for me until the end of high school.

At university, I was a true nerd. I read all my textbooks cover to cover (mainly because as I was too shy for girls and too poor for booze). During this time, the definition above started to fail. So much of the science was maths, statistics, observation, pattern recognition, logic and quite a bit of rote learning. Not all of it fitted into my definition of science. I became a fan of a new definition: science is the study of the nature of reality .

But then I did post-grad, and I realised that not much in science is ‘proven’ (I guess this is the point of post grad study). Evolution, for example, is not proven. That the sun revolves around the earth is not ‘proven’. I discovered that the only things that could be proven were ‘ideas’ about ‘other ideas’. Bear with me on this one.

Let us say we define the number system – this is an ‘idea’ or conceptual construction. Within this construction we can ‘prove’ that one and one is two. Because we ‘made’ the system, with rules, then we can make factual and true statements about it. We can’t do this about the real world – we cannot say anything with absolute certainly because we rely on flaky inputs like our own highly fallible perception.

It’s like that old chestnut: how can you be sure you are not living in a giant simulation? Of course you can argue that it is pretty unlikely and I would agree, and right there we have a clue to a better definition of science.

It turns out that much of modern science deals in ‘likelihood’ and ‘probability’ rather than proof and certainty. For example, we can say that the theory of evolution is very likely to be more-or-less right, as there is a lot of corroborating evidence. Science cannot be run like a law court – where the prosecution only need to reach a threshold of reasonable doubt to ‘prove’ someone guilty.

Aside for nerds: Science says you can use logic to prove things absolutely, but logic only works with ideas, and there is a breakdown between ideas and reality, so one can never prove things in reality. So it is thoroughly wrong for a court to say that someone has been proven guilty. The courts use this language as a convenience, to “draw a line under” a case as they have not found a moral way to dole out punishments based on probabilities. Imagine a world in which a murder suspect gets a 5 year sentence because the was a 20% chance he was guilty! Sports referees often operate in this decisive way, perhaps because it saves a lot of arguing!

Anyway, good science cannot just give up and say once there is consensus something passes from theory to fact. This is sloppy. We have to keep our options open – forever.

Think for example of Newton’s Laws of Motion. They are called ‘Laws’ because the scientific community had so much faith in them they passed from theory (or a proposed model) to accepted fact. But they were then found wrong. Strange that we persist in calling them laws!

It took Einstein’s courage (and open mindedness) to try out theories that dispensed with a key plank of the laws – that time was utterly inflexible and completely constant and reliable.

So it is that the canon of scientific knowledge has become a complex web of evidence and theories that attempt to ‘best fit’ the evidence.

Alas, there are still many propositions that many so-called scientists would claim are fact or at least ‘above reproach’. Evolution is attacked (rather pathetically), but the defenders would do well to take care before they call it ‘fact’. It is not fact, it is a superbly good explanation for the evidence, which has yet to fail a test of its predictions. So it is very very likely to be right, but it cannot be said to be fact.

This is not just a point of pedantry (though I am a bit of a pedant) – it is critical to keep this in mind as it is the key to improving our model.

Two great examples of models people forget are still in flux…

1) The big bang theory

2) Quantum theory

I will not go into global warming here though it is tempting. That is one where it doesn’t even matter if it is fact, because game theory tells you that either way, we better stop making CO2 urgently.

Back to the big bang.

I heard on the Skeptic’s Guide podcast today about an NSF questionnaire that quizzed people about whether they believed the universe was started with a massive explosion, and they tried to paint the picture that if you didn’t believe that, then you were ignorant of science. This annoyed me, because the big bang theory is now too often spoken of as if it were fact. Yes, the theory contributes viable explanations for red-shifted pulsars, background radiation, etc, etc, but people are quick to forget that it is an extrapolation relying on a fairly tall pile of suppositions.

I am not saying it is wrong, all I am saying is that it would be crazy to stop exploring other possibilities at this point.

You get a feeling for the sort of doubts you should have from the following thought experiment:

Imagine you are a photon born in the big bang. You have no mass, so you cannot help but travel at ‘light speed’. But being an obedient photon, you obey the contractions in the Lorentz equations to the letter, and time thus cannot pass for you. However, you are minding your own business one day when suddenly you zoom down toward planet earth and head straight into a big radiotelescope. Scientists analyse you and declare that you are background radiation dating from the big bang and that you have been travelling for over 13 billion years (they know this because they can backtrack the expansion of the universe). Only trouble is, that for you, no time has passed, so for you, the universe is still new. Who is right? What about a particle that was travelling at 0.999 x the speed of light since the big bang? For it, the universe is some other intermediate age. So how old is the universe, really?

This reminds us of the fundamental proposition of relatively – time is like a gooey compressible stretchable mess, and so is space, so the distance across the universe may be 13.5 billion light years, or it might be a micron (how it felt to the photon). It all depends on your perspective. It is much like the statement that the sun does not revolve around the earth and that it is the other way around. No! The sun does revolve a round the earth. You can see it clearly does. From our perspective at least.

Now, quantum theory.

Where do I start? String theory? Entanglement? Please.

The study of forces, particles, EM radiation and the like is the most exciting part of science. But being so complex, so mysterious, so weird and counter intuitive, it is super vulnerable to abuse.

Most people have no idea how to judge the merits of quantum theories. Physicists are so deep in there, they have little time (or desire or capability) to explain themselves. They also love the mystique.

I do not want to ingratiate myself with physicists, so I will add that the vast majority have complete integrity. They do want to understand and then share. However, I have been working in the field for long enough to know that there are weaknesses, holes and downright contradictions in the modern theory that are often underplayed. In fact these weaknesses are what make the field so attractive to people like me, but is also a dirty little secret.

The fact is that the three forces (weak nuclear, strong nuclear and magnetic) have not been explained anything like as well as gravity has (by relativity). And don’t get me started on quantum gravity.

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Anyway, thinking about all these issues, I concluded that science was (definition #3) the grand (platonic) model we are building of reality, ever evolving to best fit our observations.

My man, Plato

That works well for me. However, I recently came across a totally different definition for science:

# 4) “Science is a tool to help make the subjective objective.”

OK I paraphrased it to make it more snappy. It was really a discussion about how science was developed to overcome the fallibility of the human mind. Examples of weaknesses it needs to overcome are:

  1. The way our perception is filtered by preconceptions
  2. How we see pattern where there is none
  3. How we select evidence to match our opinion (confirmation bias)
  4. How we  read too much into anecdotal evidence
  5. etc etc.

I could go on. So ‘science’ is the collection of tricks we use to overcome our weaknesses.

I like this definition. We are all going about, and in our heads we are building our model of the world… and its time for an audit!

Family Tree Nonsense

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For many, learning about their family tree can be a real joy and pleasure.

Realising that a long distant grandfather was in the guild of barber-surgeons, or that you have a criminal or judge or, heaven forfend, someone famous in your lineage, can be a real thrill, and provide you with significant ego-boost, or perhaps a nice feeling of belonging.

The reason why it’s so often a positive experience, is due to an interesting mathematical oversight.

What do I mean?

This fractal can teach us something about ancestry: we have more ancestors than we tend to suppose...(image credit: Northwest Liberty School http://nwls.us/)

This fractal can teach us something about ancestry: we have more ancestors than we tend to suppose...(image credit: Northwest Liberty School http://nwls.us/)

I mean that people can read anything they want from a family tree, and this is made easy by the exponential nature of ancestry.

Would you find it remarkable for someone to say they were directly descended from Isaac Newton, Henry VIII or even Jesus? Would you think more of them?

What about people who say they are ‘from’ somewhere? – “my family originally come from Brittany…”, or “my family fought in the  revolutionary war…”

Analysis…

Now anyone who knows about the maths of ancestry, knows that there is actually very little remarkable about relations with famous people, especially from a long time back. If you have two parents and four grandparents, eight great-grand parents and so on, you can guess the numbers get big quite quickly.

The American revolutionary war was around 230 years ago, so perhaps eight or nine generations[1].  Nine generations back we had perhaps 2^9 (or 512) ancestors, and their folks were probably still around you can add them to the mix (another 1024)  giving over 1500 relatives, all swanning about somewhere in the world around the time of the war.

OK, you might want to reduce the number a bit due to some folks appearing  multiple times in your tree; (yes, in-breeding happens to all of us), but the number is probably still well in excess of  a thousand.

So, with over a thousand ancestors around at the time, the chance of having at least one involved in the war is pretty darn good (especially if you are were born to US citizens). I would argue that for anyone who can trace back three generations (to your eight great-grandparents) in the US, it would be far more remarkable if they didn’t have ancestors that fought in the war.

As you get further back in time, the numbers get more serious. A thousand years back , or forty generations, the straight maths gives 1 099 511 627 776 ancestors. Of course, this is impossible, as there were not enough people in the gene pool; the real number is clearly much lower and this is due to our old friend, in-breeding – where the family tree morphs into more of a family ‘web’ and involves the majority of the (breeding) population of your “gene pool”, the group that share enough in-breeding to behave somewhat like a super-organism. Where cross flow of genes between parts of the pool becomes retarded, (most usually by geographic barriers) the pool may divide and racial difference may develop.

Of course, we live in a time of great ‘connectivity’, and the US is a great example or a melting pot, with a very ‘open’ gene pool. This means that statistically, the chance that all 1000+ of one’s ancestors were around in the revolutionary war is hopelessly optimistic (unless there were special circumstances, like a closed community with a high degree of in-breeding, as may be the case with some religious groups).

So basically, anyone who says their family is all-American, “since the revolution” is being highly selective in their analysis.

Of course, western society does tend to invest much importance in the male line – which is far more specific – and would only give a couple of  chaps alive in ~1780, and if you can indeed prove this then the claim may be considered more interesting.

However, the argument that the male line is more important in some way (such as in the forming of character, or of any particular heritable trait) is pretty unconvincing. So even if you can trace a direct male line to Isaac Newton, this is no guarantee that you will pass your physics tests! Any advantages he had, will have been diluted by the 16,000 or so other folks who contributed just as many genes.

The male and  female lines can actually be traced (using mitochondrial DNA for the female line and Y-chromosomal DNA for the male line), but though this makes it easier to trace these ancestors,  it is perhaps still unwise to assume this line is more important than the thousands of other ancestors.

In the case of the USA, there is another factor, the large family sizes, and the resulting high population growth rate. The population present during the revolution have, by all accounts, been very fruitful. That means that even if you could trace your male line right back to, say, Thomas Jefferson, the chances are, you are not unique.

The Opinion Bit…

Hard-earned privilege...
Hard-earned privilege…

I am constantly annoyed by selective analysis of ancestry. I hope that the above simple illustrations alert the reader to this trickery, or at least confirm the reader’s suspicions (or convictions) that much of this is wishful thinking. What is most important to our own ‘value’ in the world is surely what we ourselves decide to do, not what our remote ancestors may have done.

However, I cannot deny that family research is still hugely interesting, even if what it really confirms is that we are all brothers and sisters, and none of us is superior due to our ancestry.

Don’t even get me started on so-called “royalty”!

[1] How long is a generation? http://www.ancestry.com/learn/library/article.aspx?article=11152