A Revolution in Evolution

nozzferrahhtoo wrote: »

It is a factual statement. We often distill swaths of science down into one liner titles or slogans like "Big Bang" and "Survival of the fittest". And those titles and slogans lead to great misunderstandings in communication between the lay man and the scientific classes.

There you go again. The statement I called arrogant and asinine was "not understood by people lay to the subject such as yourself". Something just highlighted by Jernal, so I don't think I am alone in catching this superior nonsense.

I have no problem at all with you disagreeing with me, or anyone disagreeing with me. Where I have a problem is with your constant need to cast aspersions on someone's else knowledge, generally based on your own interpretation of words or misunderstandings of the context another poster is using them in.

A good example is this definition of yours of environment. You are defining environment too narrowly entirely as it applies to evolution. Selection pressure can be due to literally anything, as long as it impacts survival or reproductive rates of a species, but all selection pressure is environmental. Not just what we commonly think of as environmental stress, but competition from other species, competition for mates within species, predators, etc. This is all environment as it is commonly discussed in evolutionary literature.

Yes, my fish metaphor was a poor one, but your reaction to it shows your overriding urge to try and put down your perceived "opponent", and you have the neck to accuse me of "acting like it is a personal affront". Perhaps if you left out the personal taunts of "layperson" we might have a more productive discussion.

nozzferrahhtoo wrote: »

An attempt to go back on topic would be nice so this deserves a separate post following my last.

Well, thank goodness for that:cool:.

nozzferrahhtoo wrote: »

It is still unclear at this point why you brought intelligence, or any discussion of intelligence, into the topic. You gave a long arbitrary definition of intelligence but no aspect of evolution seems to match that definition in any way at all. Nor have you attempted to make a link. So for the 4th or 5th time I much express curiosity as to what your aim or goal or point was there. It is still entirely opaque.

Let me address "adaptive" first and I will come back to "intelligence" later as it is getting late here.

nozzferrahhtoo wrote: »

What you even mean by "adaptive" is not entirely clear despite pages of posts on the matter. Are you speaking about what many writers call the Evolution of Evolovability? Are you speaking about the strong illusion of adaption that the mechanisms of evolution can give? Or are you talking about something else along the lines of foresight which your introduction of "intelligence" into the discussion would seem to suggest.

No, but I think this concept of Evolvability of Evolution will also become part of an extended synthesis in the coming years.

I am referring to the mechanisms that go on within the cell that result in either sequence changes to DNA, protein coding or regulatory regions, or epigenetic changes that impact regulatory regions without changing DNA sequence (methylation, etc.). The former are assumed to be due to errors or mutations that occur mainly during copying processes, and regarded as "random" in the sense that whether they are deleterious, neutral, or beneficial to the organism has no influence on the likelihood of them happening. In other words they are not regarded as adaptive, or happening in response to environmental stress.

However, the view that they are "random" is largely an assumption as until recent developments in Cellular Biology, we had little ability to study the actual mechanisms at the molecular level. There are experiments (Cairns, Hall, Foster) from the 1980s onwards that demonstrate adaptive mutation in E-Coli when under environmental stress, where genes were switched on, and furthermore this "change" was inherited. This was strongly opposed at the time, and alternative explanations sought, mainly because "inheritance of acquired characteristics" was explicitly excluded by the Modern Synthesis. Epigenetics is now well established within the past five years by theory and experiment as the mechanism for "inheritance of acquired characteristics".

My claim is that these two are related (the Cairns results and now epigenetics), in that they demonstrate that changes in gene expression, rather than being due to random events, are evidence for adaptive intercellular responses to environmental stress. This is further supported by the fact that the genes impacted are the specific ones that lead to a beneficial outcome (ability to process lactose in the case of the E-Coli studies), and also that the changes in gene expression are not corrected by error correction mechanisms within the cell.

I will have to return to this later.

nozzferrahhtoo wrote: »

So perhaps to pre-empt this disparity in conversations you could list for me 5 or 10 examples of the kinds of traits you are talking about, and the papers in which the trait was observed to arise and then propagate. Are ALL your examples of existing genes being turned on? Or is there a mix there with genuinely new characteristics?

I am not ignoring the rest of your post, but I think we both agree getting back to the basics of what the thread is about is a good move. I accept the criticism that I have not outlined my thinking on the subject as clearly as I should have. However, it represents a fairly significant and recent shift in my thinking, so much of this is embryonic for me at least.

I started the thread with a paper by Noble, so let me go back there again. The attached paper is one that got me started down this road and led to Jablonka and then Shapiro.

http://rsta.royalsocietypublishing.org/content/366/1878/3001.full

I think it would move the conversation along if you can review the paper and give me your thoughts. It was the "aha" moment I had in terms of moving from the selfish gene mode of thinking to the cell / organism mode of thinking. The following are the take home messages I got from reading it, and what prompted me to go looking elsewhere.

The original concept of a gene was the "thing" that transmitted inherited characteristics, and that there was a 1:1 ration between a gene and a particular phenotypic characteristic (eye color, body shape, etc.). Before DNA was discovered this "thing" was thought to be proteins. After DNA was discovered, genes became identified with specific stretches of DNA. Nobel poses a very challenging question which is if genes are equivalent to stretches of DNA, then you have to accept that the inheritance of all phenotypic characteristics is attributed to these stretches of DNA.

The main thrust of Noble's article is that there are two components of inheritance, DNA (digital information), and cellular machinery (analog information). He makes the point that if were to encode all the information in a cell to send to a distant solar system to replicate life there, the cellular mechanism data dwarfs the DNA data, and that sending the DNA alone would be like sending the bar codes from supermarket shelves to represent the produce on the shelves.

Another interesting aspect of Noble's paper is a thought experiment where you imagine dinosaur DNA being inserted into a bird's egg. Assuming the bird's egg was compatible (all attempts to my knowledge of intra species cloning have failed), then one would expect the resulting organism to be a dinosaur. This is what the Central Dogma tells us, that genetic information can only flow from DNA to protein to phenotype, or in other words from DNA to the organism.

Epigenetics changes this however as the cell does not just read DNA and follow its instructions, but also imposes patterns of markings and expression on DNA. Noble argues that by itself DNA does nothing at all, but it is cellular mechanisms, one of which is epigenetics, that determine what is expressed in the phenotype. It reverses the normal thinking of the DNA being deterministic and the cell passive.

In terms of inheritance, the egg cell (and in sexual reproduction the sperm cell) is just as important as DNA, not just in terms of any organism being produced, but what organism is produced. Where the focus on DNA has led us is in a reductionist direction or "upward causation", to the conclusion that DNA is a program determining phenotype expression, whereas when you look at cellular mechanisms the conclusion is that DNA is a database that is used by the cell, in other words the cell is in control not DNA.

The argument then becomes you have to consider both "upward" and "downward" causation, to try and get back to a meaningful understanding of the gene as the "thing" that transmits inherited characteristics. Genes defined as stretches of DNA are like pieces of re-usable lego, and have no high level functionality in themselves. The high level functionality comes from the cellular mechanisms, and it is this high level functionality that is selected in evolution. High level functionality is what determines whether an organism survives or reproduces, so the focus should be on the organism as the unit of selection and not the gene. We will only fully understand high level functionality according to Noble by reverse engineering a cell.

This is what led me to Shapiro and his theory of natural genetic engineering, which will have to wait for another post. However, I would like to emphasize I am not claiming Noble is right, or Shapiro is right, or least of all that I am right. I am saying that their work has led me to rethink my understanding of life, inheritance and evolution. In all likelihood the truth lies somewhere else, incorporating both sets of ideas, because just as I can see flaws in the selfish gene theory, I can also see flaws in Noble's arguments and Shapiro's theory.

Mark Hamill wrote: »

Yes, and my glaringly obvious point is that the patient doesn't know that. They will think it does something, even if it means the treatment would have to be supernatural to work. Prayer is probably the most common placebo there is.

As you are now repeating what I have been saying for numerous posts, I see no need to further this particular discussion. This longwinded discussion was based on your (understandable) misreading of what I meant when I said the "effect has nothing to do with the treatment", as (for at least the 10th time) the effect is entirely due to the expectation of the patient.

As you say, prayer can be a very common and effective placebo. It brings enormous benefits to millions of people. It also overlaps somewhat with neuroplasticity as the techniques used are focused thought which is somewhat analogous to prayer.

nozzferrahhtoo wrote: »

I had a nice quiet christmas myself

Good to hear. I likewise had the same, and by and large took a welcome break from internet forums. It is certainly good to recharge the batteries.

nozzferrahhtoo wrote: »

and over the last couple of weeks have had the pleasure of re-reading this thread.... your link.... and a whole host of papers on concepts like reverse RNA synthesis and the like.... which are all aspects of what many people speak about on topics like epigenetics.
And it is all fascinating stuff and I can not get enough of reading "cutting edge" papers on the subject. Yet despite it all I am not seeing this "revolution" you speak of...

Yet, after all that effort, including presumably reading Noble's paper, you have no comment whatsoever on what is being proposed i.e. that the gene centric view of Neo-Darwinism, as espoused with great clarity by Dawkins, is being shown by evidence to be completely insufficient to explain evolution. That is quite the claim, I would have thought you would have something to say on the matter, rather than dismissing the "point" of the overall thread.

nozzferrahhtoo wrote: »

.. where all this evolutionary "dogma" is remains a mystery.... and what aspects of evolution "dogma" is negates by identical twins is still being avoided..... all of this remains clouded and shady to me.

The "dogma" is that the organism is merely a carrier of the object of selection i.e. its genes, cut off from both the organism itself and its environment, and that any physiological function in influencing genetic inheritance is specifically excluded by neo-Darwinism.

The issue with identical twins is a very salient point, although a subtle one. Identical twins have identical DNA, therefore any differences during development has been thought historically to be environmental. For example, in the onset of diseases, if one smoked and the other did not, this could correlate to lung cancer in one. However, the paradoxical issue remains that phenotypic differences are seen that cannot be explained easily by environmental differences. Why are identical (MZ) twins often discordant for disease when their DNA is identical and their environment similar? Why for example do you not see the expected correlation in MZ twins for something like schizophrenia, a disease where genetic contribution is well established as the main component. This question is explored in the attached paper comparing modern data for MZ and DZ twins. The key issue here is that this type of experimental evidence has only been recently made possible by the tools now available to geneticists i.e. high throughput epigenetic analysis.

http://hmg.oxfordjournals.org/content/14/suppl_1/R11.long

nozzferrahhtoo wrote: »

I wonder if the fact that the thread itself has been quite quite dead since our last exchange on the matter is not indicative of the fact that I am far from alone in having this impression, but am merely the only one vocalizing it?

I wonder about that as well. The only conclusion I can reach is there appears to be little interest in the science of evolution, but enormous interest in creationism .

The basic "point" of this thread is that there is a third factor which likely bridges the gap in our understanding between evolutionary mechanisms and physiological mechanisms. The claim is that organisms actively respond to the stresses imposed by their environments and moderate gene expression through epigenetic and other cellular mechanisms, and these changes in gene expression which impact their phenotype can be inherited. This provides for a much more rapid evolutionary mechanism than random mutation. Nobody is questioning that random mutation does not occur, what is being questioned is random mutation as the primary source of variation in populations leading to evolutionary change.

nozzferrahhtoo wrote: »

The former claim is not new or revolutionary however. This research has been ongoing for some time. Anyone interested in it only has to, as I said above, spend a couple of weeks reading papers on the "Reverse RNA" concept.

We may be talking past each other here. Are you saying that the hypothesis proposed by Shapiro (natural Genetic engineering), and supported by Noble, is uncontroversial? Is so, this is interesting, as Shapiro's proposals are refuted quite strongly by many noted evolutionary biologists (Shapiro is a Molecular biologist, and Noble a Systems Biologist).

nozzferrahhtoo wrote: »

The inheritance of such things is a little more controversial of course. Because a mechanism for such a thing is not known at all. That things like Reverse RNA would affect Genetics at a local level is one thing... but that a mechanism exists to pass this on to the sex gametes is quite another.

The mechanisms for how the epigenome impacts gene expression during development and throughout life is reasonably well known. Up to recently it was believed that epigenetic marks and/or imprints were wiped clean during the gamete formation process. This does not appear to be the case based on the most recent research (2007 onwards).

robindch wrote: »

233 posts in and I've still no idea what this thread is about.

Assuming you have the time I would recommend the free on-line class offered by Coursera "An Introduction to Genetics and Evolution". It has just started and involves a minimum commitment of about 1 hour of lectures per week.

Even if you review the week 0 Introductory materials, you will quickly see what this tread is about. The lecturer has a good old fashioned bash at Lamark, and uses the same old tired example as a pop question to prospective students "If a person loses an arm, will their offspring be born without an arm?", and has a good old laugh at Lamark's expense.

Fortunately the next in the series is a class on Epigenetics, so hopefully Lamark's reputation can be somewhat restored.

Jernal wrote: »

That's overly harsh. He was a laughing at his old grade 10 self's expense. Where he himself had thought that if you kept cutting the arms of people eventually one of their offspring would have no arms. In no way did it come across as a slight against Lamark. It was only an example used to convey a basic principle with a bit of self deprecating humour.

Fair point, it was a little harsh. However, he did say that in the 10th grade he believed in Lamarkian style evolution in a response to a question, and this was shown to be incorrect. Given the recent research into "inheritance of acquired characteristics" via epigenetic mechanisms, it would in my view have been appropriate to say that it now appears Lamark was partially right, he just did not understand the underlying genetic/epigenetic mechanisms involved, no more so than Darwin did.

The slight against Lamark was using the "Lamark was wrong because of giraffes and blacksmiths" examples, buttressed by his own loss of arms example, without adding the caveat that recent research is forcing us to reconsider Lamark.