跟读练习: "What is life"-lecture: Denis Noble - 通过视频学习英语口语

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Well, thank you very much, Peter, for that introduction.
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And let me say what a huge pleasure it is to come back to the Karolinska Institute.
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The last time I was here I think was about three years ago for a meeting on systems, biology and cancer.
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You know, I'm always asked to talk about subjects about which I have no right to claim any knowledge whatsoever.
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Interestingly enough at that meeting I think quite a lot of other people thought exactly the same.
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We had a very interesting meeting.
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What I'm going to do today is to address Schrodinger's question,
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which of course was the question, what is life?
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those
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lectures were given in 1943 at the Dublin Institute of Advanced Studies
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and they were of course the lectures in
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which Schrodinger first made his famous prediction that the genetic material would be what he called a non-periodic crystal
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I still, and I think many others do too, still think that's an extremely good description,
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of course, of what was eventually found in the DNA.
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He also, though, drew a comparison between, on the one hand, physics, and on the other hand, biology.
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And his idea in that book was that they were really very different.
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because physics deals with order emerging from disorder.
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You have the disorder of the random movements of the molecules of a gas, but you also have the order of the gas laws and of thermodynamics.
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By contrast, he argued, biology is about order from order, because where is the order down at the low level,
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it is in that aperiodic crystal.
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And I think his idea gave rise, of course, later on, or helped to give rise,
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to the interpretations that were made of the early results in molecular biology of DNA
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when the double helix was discovered and when people began to work out what the coding was between DNA and proteins,
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which was to lead to the idea that there was, in a sense, in the DNA, a determinant program.
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So unlike physics, you would go from particular events in molecules to particular events in the global property of the organism,
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that is, the phenotype.
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Now, of course, it's a hard thing to say that perhaps Scherzinger was wrong, but I think he was.
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And I would like to substitute that, the view that I and many others now express about biology,
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and it's certainly expressed in the book The Music of Life,
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which is that indeed physics deals with order from disorder,
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but biology also must most of the time do the same
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because what do we find down at the level of the individual gene expressions?
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We find stochasticity.
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If I take the gene expression levels in the ventricular cells of one region of the heart
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and compare them to the expression levels of those genes in an adjacent region of the heart,
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I will find that they vary.
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Now, of course, they vary to some extent according to the anatomy of the heart, and that is both well known and is also important in the functioning of the heart.
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but they also vary stochastically, even between neighboring cells.
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Stochasticity, therefore, has to be a feature of biology as well as order.
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Of course, we have a little bit of a dilemma, which I'll refer to a little bit later on,
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which is that we know well that there are certain changes that occur down at the molecular level,
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particular mutations which will produce or be the cause of a major change in function at the level of the phenotype.
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But what has emerged in the research that's been done over the last decades is that those cases are actually quite rare.
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I find that in my work on the heart.
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There are certain modifications, certain mutations of particular ion channels that can produce a catastrophic situation predisposing towards arrhythmia.
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But most of the time, the heart works perfectly well, just as the pancreas does, just as the brain does,
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despite all the variations that occur at the lower levels.
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So why should a physiologist be concerned about the question, what is life?
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First of all, to be concerned with that, you have got to be concerned with the central theory of biology
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or the central story of biology because I think that what we call evolutionary theory is actually a story,
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it's a history, which of course is the central idea
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without which any form of discussion of the question of what is life can't make sense.
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moreover the dominant theory of evolution over most of the 20th century and into this century was of course the modern synthesis
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sometimes called neo-Darwinism and
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that of course was a gene-centered theory of evolution with its determinate idea of there being a program
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that leads to the development of the organism
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but in fact organisms are extremely good at immunizing themselves from
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variations in their genomes we're going to look at a few examples of
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that in just a moment and some of the examples are discussed in
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that article in the Royal Society's new journal Interface Focus
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let's just give a little bit of background from my own work
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as the introducer said I was responsible for working on some
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of the early discoveries of ion channels in the heart and
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that led me to put this model of rhythm in the heart together in 1960.
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Here's the electrical potential showing rhythm that emerges as a cell property not a molecular property from the interactions
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between the various ion channels.
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In those days, we actually thought there weren't many more channels than there are in nerve.
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A sodium channel, two potassium channels, and a background leak.
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We now know there are many more.
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And in fact, later on, if we go now through to about 25 years later,
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in work that I did with Dario Di Francesco, we found there were many, many more potassium channels than we thought initially.
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And of course, by that time, Harold Reuter had made his great discoveries of calcium channels and of sodium-calcium exchange.
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We were also responsible in the work with Dario Di Francesco at discovering a new non-specific cation channel,
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which is responsible for this phase of the rhythm, and also for clarifying the role of the sodium-calcium exchange.
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Now, that's all technical detail and I don't want to dwell on that.
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What I want to do is to use that model to perform a very interesting experiment.
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So what we're going to do is to use a version of
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that model that was developed for the natural rhythm generator of the heart, which is the sinus node.
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and I'm just plotting two of the channel properties,
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a background sodium channel and the non-specific cation channel that I referred to earlier.
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This one normally contributes about 80% of the depolarizing current.
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It is therefore the rhythm generator, if you like.
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And as you knock it down, you can notice 20%, 40% all the way to complete knockout.
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You might expect a very large change in frequency.
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In fact, the change in frequency is very modest, only about 10%.
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And what is happening, of course, is the system is allowing this other mechanism to kick in and to keep the rhythm buffered,
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as it were, from the change at the lower level.
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And you can even use the physiological interpretation of what is going on to work out what is happening
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because if you draw a line along those voltage traces,
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you can see that the traces at this end are moving into a more negative range of electrical potential.
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And it's precisely that that activates the other channel to kick in and to keep the rhythm fairly constant.
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And that is a general property of cardiac rhythm.
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It's a general property of other rhythm generators too, for example, of circadian rhythm.
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There are backup mechanisms.
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Many more examples of what you might call knockout that don't actually succeed in producing a very large phenotypic effect.
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This is from some work, again fairly technical detail, but I won't dwell on the technical detail other than to say
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that a targeted knockout done in experiments first and then by simulation reproducing the experiments of Ken Philipson,
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targeted knockout of the sodium calcium exchange produces almost no change in overall electrical function.
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Now, is this a specific property of some of Dennis Noble's work on the heart or is it general?
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I was delighted therefore when I saw this systematic study by Hillenmayer and his colleagues in yeast working
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through the 6,000 genes and producing what they called a chemical genomic portrait of yeast.
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What did they find?
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Genetic buffering is general.
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80% of the knockouts are silent under normal physiological conditions.
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That doesn't mean to say that those genes don't have a function far from it.
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They do code for a protein.
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That protein is produced.
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of course what you have to do if you want to reveal that function is to stress the organism
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for example with metabolic stress
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and then you can begin to reveal the function there are many more examples I won't dwell on
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that other than to say that if you want to understand regulators in biological systems
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which is part of an answer to the question what is life life is a regulated process
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then you don't get that most of the time from knockout experiments.
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As I said earlier on, sometimes you do.
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Biology therefore is a mix.
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Occasionally it is order from order
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but often it is also order from disorder in a sense
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just like physics though I think there are some important differences as well.
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For those who want to follow up on that question and this lovely article in bio-essays is worth reading.
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So what is going on?
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And here I want to also digress a little bit on the concept of a gene, because I think two things are going on here.
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First of all, extensive buffering of organisms against genomic change.
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that's now documented I think sufficiently well to say that it's a fairly general phenomenon
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but there's another major concept that I want to introduce
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which is that the concept of a gene has changed
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and changed in a very significant way indeed
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and it's central to understanding what is wrong with current evolutionary biology theory that is the neo-Darwinist theory.
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The way I explain this is to say that we have DNA, obviously, we have a phenotype.
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Of course, it's a bit artificial to draw complete distinctions between the two.
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As I will quote with Barbara McClintock later on, the DNA is also, after all, a part of the phenotype.
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But I think we all know what we're saying here.
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Here's the genetic material in the sense that the molecular biologists would use that term today.
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Here's the interaction with the environment.
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Here is, if you like, the complete phenotype.
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And what we know is, of course, that all of these interact in bidirectional ways.
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That's also important with the biological networks, the signaling pathways, the filters, the conditioners, and so on,
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which actually generate the function.
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If we want an answer to the question, therefore, what is life?
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it's inside here.
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If I take the DNA out of a cell, if I could do just that and put it into a Petri dish,
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I could keep it for 10,000 years and it would do nothing.
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It's the rest of the system of course that tells the genome when it wants to make particular proteins.
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It's the rest of the system that gives the dynamism.
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Now I come to the point about the definition of genes When Johansson in 1909 first introduced the word gene,
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of course following in the footsteps of Mendel, who didn't use that word but he had exactly the concept,
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what he actually meant was a discrete inheritable phenotype.
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What we now mean of course by a gene is a particular stretch of DNA.
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Now the important point I want to make is that not only are those two definitions not the same,
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that's obvious from the fact that this only includes this part of the diagram, whereas this includes the whole diagram,
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they are conceptually different too.
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Because Johansson's definition is all-inclusive.
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He actually says that in his article.
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He says, it's a something.
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it doesn't really matter whether it was DNA or not of course they did not know about DNA at that time
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incidentally Richard Dawkins uses exactly the same definition most of the time as Johansson
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he also says it is as it were a general concept it is if you like a catch-all concept
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but of course the problem with catch-all concepts that say and include everything is that they can't be tested
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it is a necessary truth
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a conceptually necessary truth that a gene defined in this way as the cause of a particular phenotype characteristic is just that,
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it is the cause you don't ask the question, is it a cause it is so by definition now, the situation of course with the definition of a gene
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that is done in terms of a DNA sequence is that precisely that question can be asked
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There is an empirical question to be settled, which is, does that particular piece of DNA have a big effect on the phenotype?
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You can perform that experiment with the kinds of knockout experiments that I've already described.
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So the difference is fundamental.
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Now, where is the deep problem in the neo-Darwinist thesis,
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particularly as expressed by people like Richard Dawkins in popularizing it.
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The problem lies here, that if you want to distinguish clearly and unambiguously between the replicator,
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which is of course the DNA, and the vehicle, which of course is the organism that carries the DNA,
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then you must use this definition of the gene.
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If you use this one, the one that Johansson first introduced then it doesn't make sense to draw a distinction between the replicator
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and the vehicle because this definition includes much more than the DNA and I don't think that point has been properly appreciated.
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In relation to knockout experiments of course to represent the fact
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that most knockouts and mutations are buffered
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but knocking out just one gene may not get through to the phenotype
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because it gets absorbed as I showed in those computations
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but also in the experiments on which they're based a bit earlier
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but two of course may be enough to get through
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or you may need to do three who knows that's a matter open to empirical investigation
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so I want to turn now to a few other aspects in which the answer to the question what is life
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taking particularly evolutionary biology as absolutely central to that question and to answering it properly
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poses today some very big problems
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but what we need to do is to first go through a very brief history of evolutionary biology
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And I start by going back just over 200 years to Jean-Baptiste Lamarck, who published the Zoologie Philosophique,
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his great work in 1809, exactly 50 years incidentally before Darwin's Origin of Species.
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Jean-Baptiste Lamarck actually invented the term biology he was one of
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those who first as it were therefore defined our subject as a separate subject from other natural science subjects
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but he also did something else which is very famous he certainly espoused and popularized and used
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the theory that there was inheritance of acquired characteristics.
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And many of you will know that, of course, it is a clear feature of the modern synthesis
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or of neo-Darwinism that that process is excluded for reasons I'll come on to a little bit later.
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Darwin, of course, published his Origin of Species in 1859, proposed, of course, the theory of natural selection.
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of course neither he nor Lamarck or anybody else at
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that time had a theory of genetics and heredity in
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that sense they didn't know of Mendel's work until it was rediscovered later now an important point to make
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Darwin also assumed the presence
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and function of the inheritance of acquired characteristics it's present in the origin of species in 12 different places unambiguous,
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all documented incidentally by Ernst Mayer many years ago in his great book Biological Thought in 1982
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further Charles Darwin in I think it's the fourth edition of
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The Origin of Species specifically praises Lamarck as this great biologist who championed the idea
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that there was transformation of species originating from a common ancestor
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Darwin was not a neo-Darwinist that's a very important message we'll come on to the significance of
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that a bit later on so what gave rise to neo-Darwinism?
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what gave rise to neo-Darwinism was of course the work of Weissman who introduced the idea
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which we now call the Weissman barrier that is the specific exclusion of the inheritance of acquired characteristics.
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And the idea was, of course, that the inherited material, wherever it was, and of course he didn't know where it was at that time,
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is immune from the rest of the system.
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The rest of the system, however it develops in the lifetime of an individual, cannot influence the genome, as we would now call it.
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And of course that later became encapsulated in Francis Crick's idea of the central dogma of molecular biology.
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let me just also make a brief explanation at this point in the paper in
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which he defines the central dogma in 1970
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Crick was actually very careful he referred to the fact
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that of course DNA sequences code for protein amino acid sequences
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but amino acid sequences do not code for DNA sequences In that sense, there is a unidirectional flow of information.
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But he did not make the mistake, which was made later by Dawkins and many others,
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of assuming that that meant that no information passes in the other direction.
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And of course, if you ask the question, what makes your heart cell different from your pancreatic cell, different from your liver cell,
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It is precisely the passage of information from the system onto the genome
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to tell the genome to make a completely different pattern of gene expression in a heart cell, a pancreatic cell, a liver cell, a bone cell, and so on.
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So we know already, even just from that observation alone, that there must be information passing the other way.
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We'll come on to the significance of that also a little bit later.
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all of this was put together by Julian Huxley, Fisher, Haldane, Sewell Wright and others
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to form what was called the modern synthesis and it's the modern synthesis
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that is often also called neo-Dawinism now let's look at the popularisation of it in the selfish gene
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I should say that I've interacted with Richard Dawkins on these issues now, ever since he published The Selfish Gene.
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In fact, I've interacted with Richard Dawkins even before he published The Selfish Gene.
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What is it?
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It is, of course, a gene-centered view of natural selection.
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That is what the modern synthesis is.
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Accumulation of random mutations.
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By random here is meant not related to function.
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Random compared to function then followed by selection.
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That means, incidentally, that physiological science has nothing to say about the variation in genetic material.
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Very important, because we'll see that that view is actually wrong.
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Then the impossibility of the inheritance of acquired characteristics, a view, of course, inherited initially from Weissman and the Weissman barrier,
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and then later on buttressed and supported by the more popular interpretations of the central dogma of molecular biology.
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Now, I say that's miscalled Lamarckism because actually,
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if you look at the history of the idea of the acquisition of characteristics that can be inherited,
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that idea was not Lamarck's invention.
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Many others before Lamarck had said the same thing.
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Lamarck, like Darwin himself, just simply assumed it.
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They didn't invent it.
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Neither of them did.
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The other point that I've emphasized earlier on is the distinction between the replicator genes and the vehicle, the phenotype.
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And notice what I said earlier on, I'll just repeat it now.
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The only way in which that distinction can be clear is if the gene is defined as DNA, as what we would now today call the replicator.
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So the vehicle is separate from the replicator.
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If, as Richard also does,
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you see, you define gene to be the original definition by Johansson and implied, of course, by Mendel, though he didn't use that word,
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then you cannot make that distinction.
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There's no way of having it both ways.
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You either define genes in terms of the DNA replicator, and then you have a clear distinction between replicator and vehicle,
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or you define genes in the way that Johansson originally did in terms of phenotype
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and then you can't have such a clear distinction.
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And as I said earlier, these ideas were buttressed by what I would call misinterpretations because I don't think they were intended by Francis Crick,
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misinterpretations, the central dogma of molecular biology.
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Now, the main point of my talk today on the question, what is life, is that to answer that question we have to realize
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that all of these rules have now been broken in ways that I'll just go through.
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First of all, are mutations random?
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The answer is no, and by a very long way.
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In his book recently published, the book by Jim Shapiro in Chicago, Evolution of You from the 21st Century,
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writes it's difficult if not impossible to find a genome change operator that is truly random
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in its action within the DNA of the cell where it works.
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But I want to go a bit further than Jim does.
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Jim documents with very, very many examples from the empirical literature,
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scientific literature, the non-random nature in the sense that there are hot spots in the genome,
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there are great big reorganizations of the genome whole domains as we'll see in a moment
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that have shifted around in the course of evolution
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but I think he fails to make an important distinction
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which has to be added to this which is the big question
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the big question that should worry the neo-darwinists is some of
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that non-randomness functional in other words can the functional state of the organism influence the DNA
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and we'll see in a moment that it can
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he also makes the point which I want to emphasize that
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if you look at what emerged from the first sequencing of
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the human genome you find a very interesting fact for two major classes of proteins transcription factors
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and chromatin binding proteins the evidence is
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that they could not have evolved one mutation at a time in a gradual way as the
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is in accord with the spirit at least of the modern synthesis or neo-Darwinism.
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This diagram is a little bit technical so I'll just go through it very, very quickly.
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All you need to know is
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that these are representations of particular proteins in different organisms all
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the way from yeast through worm through to the human and the stars that I'm going to put up now
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are whole domains, that is long stretches of DNA that have clearly moved around in the course of evolution as whole domains,
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not gradual accumulation of mutations, point mutations or small mutations.
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And as you can see, there are many of them.
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And the same is true for the other class of proteins that they studied.
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So proteins, not all of them anyway, did not evolve just via gradual mutation.
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Something is enabling the system to reorganize the genome.
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So the question I'm going to ask now is what happens in this view to selfish genes.
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And again, I come now to a deep conceptual error.
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the problem with the selfish gene is very simple
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the book is written beautifully
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anybody who's read Richard Dawkins books must admire the skill
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that he has in expressing the view that he expresses and the way in which he uses language
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they're brilliant books but when he was asked the question is selfish,
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in the title of the selfish gene, metaphor by the philosopher Mary Mitchley.
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He wrote back, that was no metaphor.
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I believe it is the literal truth.
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But then he went on to write this very significant qualification.
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Provided certain key words are defined in the particular ways favoured by biologists
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and if you've been thinking about the question what is a metaphor?
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A metaphor is precisely taking a word from one context and changing it and making it perform a new function.
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It is a way, if you like, of redefining a word.
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Clearly, in writing this, he didn't understand the question that Mary Midgley was putting to him, was it a metaphor?
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It clearly is.
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He didn't think it was.
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I wrote about this more recently in an article published in the Journal of Physiology just three years ago, and a quote from it is
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that a metaphor does not cease to be a metaphor simply
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because one defines a word to mean something other than its normal meaning.
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It indeed is the function of metaphor to do precisely this.
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and so at the heart of the neo-Darwinist synthesis at the heart of its popularization
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there are a number of major conceptual mistakes
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first of all a mistake about what is the real definition of a gene
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and it slips between the two according to what the question is
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and you can't do that you can't do that and be logical
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and second because as I show in that article
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but I don't have the time to go through all of
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that in the lecture it's actually impossible to demonstrate any biological experiment that would distinguish the selfish gene theory from any alternative
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and incidentally, curiously enough, Richard Dawkins agrees with that in Extended Phenotype,
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he writes specifically I doubt whether there is any experiment to prove my case.
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So that aspect, at least, of the neo-Darwinist approach to the question, what is life, is simply not falsifiable.
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Now we come to the big question, and the difficult one, can acquired characteristics be inherited?
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I discussed this a number of years ago with John Maynard Smith.
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We were both at the Novartis Foundation Symposium.
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He published a lovely book called Evolutionary Genetics in 1998, and he made a very interesting statement.
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he said John Maynard Smith although he was working totally within
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the neo-Darwinist view he was I think a great thinker and he said in that book specifically
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you know Lamarckism is not so obviously false as it's sometimes made out let's have a look, he was absolutely right although he didn't know
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that at the time there are many examples now those who
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want to go to my Music of Life website will find a page devoted to what are called answers,
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answers to very common questions on this central issue, the theory of evolution and the question, what is life?
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And although I'm just going to give a few examples in this slide, there are many more on that page.
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Weaver's work looking at the way in which you can mark the genome by behavior in each generation.
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and that can work even if nothing goes down through the germline.
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Anway and his colleagues looking at endocrine disruptors where the process does go down through the germline
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and we think probably through inherited RNAs.
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This paper also showing male transgenerational responses in the human.
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Beautiful paper by Yunhua Sun and his colleagues at the Fish Institute in Wuhan in China.
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doing cross-species cloning.
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I'll show that in a moment in another slide.
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And an extraordinary study by Harry Harvey and his colleagues in Cell, published around three years ago,
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showing not only transgenerational inheritance of an acquired RNA-based response,
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but also that it persists for a hundred generations.
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They followed it in C elegans for a whole year.
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the usual reply of neo-Darwinists to these examples is to say the effects die out
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well they don't always die out
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and then they will say well it's rare indeed it is as far as we know at the moment
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but remember also that speciation is rare
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it doesn't have to happen very often it hasn't happened in our lifetimes it hasn't happened in the lifetime of humans
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in fact we've tried very hard with artificial selection of dogs, cats, fish and so on we've produced new varieties but never new species
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so environmentally induced changes can be inherited I think the evidence for
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that as I said is now growing very rapidly go to the answers page on the Music of Life website
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if you want more details I said I'd say what happens in cross species clones
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and then we come towards the end of the lecture
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what Jung Ha Sun and his colleagues did in Wuhan was to take a carp which is this one,
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a goldfish and proceeded to take the nucleus from a carp
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and insert it into the fertilized
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but then enucleated egg cell as the goldfish you should get unambiguously a carp
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if the neo-Darwinist view is correct what you get is intermediate
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this is the result it's one of the few examples where a cross species works in the sense
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that you produce an adult and what it produces is an adult whose anatomy is intermediate between the two
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you can even quantify that if you look at the total number of vertebrae in the goldfish it's about 26
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there is up or down 1 or 2 and the carp is about 33
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in the cross species clone you get a figure in between but it's closer marginally to that of the goldfish.
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There are other respects also in which what they call the inheritance of cytoplasmic information is clearly occurring.
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And I want to come now to one of the greatest thinkers about genetics and their relation to the phenotype.
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I have a lovely picture in my office in Oxford of
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Barbara McClintock at the age of about 81 I think receiving
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the Nobel Prize here in precisely this lecture theatre standing exactly where I'm standing at the moment
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and she was giving of course her Nobel Prize lecture which she received in 1983
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She was of course the person who discovered what we sometimes call jumping genes or mobile genetic elements but she went much,
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much further than that until she was, I'm sorry to say, prevented from publishing.
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From 1953 onwards she no longer published on this issue until, as far as I can recall,
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she was awarded the Nobel Prize in 1983.
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She wrote in that lecture, in the future attention will undoubtedly be centered on the genome
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and with greater appreciation of its significance as a highly sensitive organ of the cell.
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The result of her work on maize was to show her just how labile the material is,
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the genetic material is in response to environmental events.
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And she wrote, responding to those often by restructuring the genome.
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Here we come back to what Jim Shapiro was drawing attention to, that clearly during evolution there have been major restructurings of genomes,
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movements of whole domains corresponding to various proteins.
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So cytoplasmic changes can be inherited,
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and I'll deal, I think I'll jump straight to the next slide just to give one example of how strong
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that inheritance can be.
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This is the article I would recommend reading if you want what I would regard now as the best example of that,
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published by Joe Nadeau's lab at that time in Seattle in PNAS at the end of 2012.
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They write, I won't go through the full details,
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the heritable epigenetic changes persisted for multiple generations and were fully reversed after consecutive crosses through the alternative germline image.
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So my main conclusion, environmentally induced changes can be inherited to the question, are they fairly rare?
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I would give the response I gave earlier on, so is speciation. so
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when we ask the question do we know what the precise
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mechanisms of speciation were I think the honest answer is that we don't know
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not yet anyway
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now I come to my final conclusion
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if functional changes in the adult can be inherited and therefore a target for natural selection
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then the analysis of function is highly relevant to evolution and of course highly relevant to defining the question
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or an answer to the question, what is life?
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Because as I said earlier on, this area of biology is central to understanding the answer to that question.
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I think what I want to do is to leave time for discussion.
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I'll just jump the remaining slides.
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They just simply summarize what I've already just said.
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And the synthesis that I would propose is shown here that we have to recognize that selection is multi-level,
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that acquired characteristics can be inherited to quote Barbara McClintock the
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genome is an organ of the cell not its dictator and that genomes are not isolated from the organism and environment
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those who want to listen to another version of this lecture it's on the Music of Life website and on YouTube
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and the article there published just last year
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in experimental physiology also gives chapter and verse on almost everything that I've presented today.
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And I finish with this lovely picture that I used right at the beginning.
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Some of you will recognise the left-hand picture as Conrad Waddington's beautiful picture from the strategy of the genes
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in which he tried to explain the way in which there is plasticity at the developmental level in the phenotype,
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which is representing by a landscape here,
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as a consequence of various gene products interacting in networks that,
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as it were, are situated between the genome level and the phenotype level.
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I know that's a bit artificial.
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We can argue about the exact definition of a phenotype and so on.
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But he's got the message.
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He's got exactly the system's approach to it.
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What happened to Conrad Waddington, he was largely ignored, pushed to one side,
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just as Barbara McClintock was until she received the Nobel Prize.
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So my final question is, who pulls strings?
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In any multi-level set of interactions in any biological organism,
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the answer is, everything can.
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if you take a three dimensional network just put together some knitting
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and make a three dimensional knitting structure you pull any bit of it the whole network changes all networks do that
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so it doesn't make sense to isolate one part and say
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that is the cause if you have networks as part of the definition
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and processes in those networks as part of the definition of an organism
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then the answer to the question what is life is it lies in those processes in the networks.
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There is no privileged level of causation.
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And with that, thank you very much.
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The end of the lecture.
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Thank you.

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