A Revolution in Evolution

nagirrac

To get away from the madness of the Noah's Ark thread, I thought it might be worthwhile to discus the science of evolution and how some of the most recent research is shaking up the field (maybe not quite a revolution yet sarky, but revolutions can take a while to get going:)).

To introduce the topic, the modern synthesis or Neo-Darwinism was developed in the 1920s-1940s (Fisher, Haldane, Wright, Huxley) as Mendel's genetics was integrated with Darwin's theory of gradual evolution via natural selection or descent with modification. The basic assumptions of the modern synthesis were as follows; 1) the mechanism of change was random mutation of genes (DNA was unknown at this time) brought about mainly by copying errors, 2) genetic change by random mutation is gradual and thus evolution generally proceeds very slowly, 3) gene variants (allenes) that result in an advantage are selected i.e. survival of the fittest, and 4) characteristics acquired during the lifetime of an organism are not inherited i.e. not alone will a dog who has had its tail cut off not produce dogs without tails, but a giraffe who stretches its neck to reach higher vegetation will not result in longer necked offspring.

The modern synthesis was added to with each discovery, DNA being the most significant. This led to the gene centric view of evolution in the 1970s, based on the work of Hamilton, Williams, and Maynard Smith, and popularized by Dawkins' The Selfish Gene, which claims that the genome (the collection of genes that results in a specific organism's phenotype) is cut off from the outside world completely, and that genes are the sole unit of selection, or the dictator of evolution if you like.

The attached paper summarizes the research over the past 5 - 7 years that seems to be dismantling the modern synthesis. Of particular note is that fact that considerable evidence now exists that acquired characteristics are inherited and can persist for multiple generations. The conclusion of all of this research, according to James Shapiro, is that rather than vehicles for genes, cells and by extension organisms actively modify their genome in response to inputs from their environment, or what he refers to as "natural genetic engineering". Although random mutation exists, there is nothing random about the majority of mutations leading to evolutionary change, and there is nothing gradual about evolution, change can be very rapid when the environment changes. While DNA can be damaged by mutation, cells guard to an incredible extend against such mutations, and have two separate error correction mechanisms which reduces the possibility of errors due to random mutation to 1 in a billion. The fact that identical genotypes gives rise to different phenotypes (in identical twins) i.e. organisms with different morphology and physiology, discredits the central dogma of evolution.

The conclusions of Shapiro's work is that all organisms are sentient, are intrinsically teleological (tending towards a goal), and nature acts like a genetic engineer. For obvious reasons Shapiro's work has been jumped on with gusto by ID proponents and beaten about the head by some traditional evolutionary biologists, who regard him as a heretic (some of the comments towards him on Jerry Coyne's blog are simply vicious), but it is based on an increasing amount of experimental evidence and thus bears serious consideration. Shapiro is far from a creationist, what he is proposing is a natural teleological explanation for evolution. For some reason this hypothesis backed by experimental evidence is regarded as blasphemy, sound familiar?

http://ep.physoc.org/content/early/2013/04/12/expphysiol.2012.071134.full.pdf

nagirrac

OK I'll just put this here as apparently this is the place for scientific discussion.



To get away from the madness of the Noah's Ark thread (sorry, get back to science), I thought it might be worthwhile to discus the science of evolution and how some of the most recent research is shaking up the field (maybe not quite a revolution yet sarky, but revolutions can take a while to get going).

To introduce the topic, the modern synthesis or Neo-Darwinism was developed in the 1920s-1940s (Fisher, Haldane, Wright, Huxley) as Mendel's genetics was integrated with Darwin's theory of gradual evolution via natural selection or descent with modification. The basic assumptions of the modern synthesis were as follows; 1) the mechanism of change was random mutation of genes (DNA was unknown at this time) brought about mainly by copying errors, 2) genetic change by random mutation is gradual and thus evolution generally proceeds very slowly, 3) gene variants (allenes) that result in an advantage are selected i.e. survival of the fittest, and 4) characteristics acquired during the lifetime of an organism are not inherited i.e. not alone will a dog who has had its tail cut off not produce dogs without tails, but a giraffe who stretches its neck to reach higher vegetation will not result in longer necked offspring.



The modern synthesis was added to with each discovery, DNA being the most significant. This led to the gene centric view of evolution in the 1970s, based on the work of Hamilton, Williams, and Maynard Smith, and popularized by Dawkins' The Selfish Gene, which claims that the genome (the collection of genes that results in a specific organism's phenotype) is cut off from the outside world completely, and that genes are the sole unit of selection, or the dictator of evolution if you like.



The attached paper summarizes the research over the past 5 - 7 years that seems to be dismantling the modern synthesis. Of particular note is that fact that considerable evidence now exists that acquired characteristics are inherited and can persist for multiple generations. The conclusion of all of this research, according to James Shapiro, is that rather than vehicles for genes, cells and by extension organisms actively modify their genome in response to inputs from their environment, or what he refers to as "natural genetic engineering". Although random mutation exists, there is nothing random about the majority of mutations leading to evolutionary change, and there is nothing gradual about evolution, change can be very rapid when the environment changes. While DNA can be damaged by mutation, cells guard to an incredible extend against such mutations, and have two separate error correction mechanisms which reduces the possibility of errors due to random mutation to 1 in a billion. The fact that identical genotypes gives rise to different phenotypes (in identical twins) i.e. organisms with different morphology and physiology, discredits the central dogma of evolution.



The conclusions of Shapiro's work is that all organisms are sentient, are intrinsically teleological (tending towards a goal), and nature acts like a genetic engineer. For obvious reasons Shapiro's work has been jumped on with gusto by ID proponents and beaten about the head by some traditional evolutionary biologists, who regard him as a heretic (some of the comments towards him on Jerry Coyne's blog are simply vicious), but it is based on an increasing amount of experimental evidence and thus bears serious consideration. Shapiro is far from a creationist, what he is proposing is a natural teleological explanation for evolution. For some reason this hypothesis backed by experimental evidence is regarded as blasphemy, sound familiar?



http://ep.physoc.org/content/early/2013/04/12/expphysiol.2012.071134.full.pdf

nagirrac

Just talking to myself here while waiting for all those with a genuine interest in evolution to wake up..

The big problem in all discussion around evolution is the confusion between the fact of evolution and the theory of evolution (tips hat to Zombrex in memory of many debates on this subject). The fact of evolution is that all organisms on earth that are currently living or were once living, descended from a common ancestor or small group of ancestors. The theory of evolution, of which Darwin's was the first comprehensive one, tries to explain the mechanisms involved in how a single celled organism evolved into the myriad of complex life forms that exist, culminating in ourselves for the time being at least.

What the latest research is telling us is that Darwin's theory alone of modification (later clarified as random mutation of DNA) leading to natural selection is hopelessly inadequate in explaining evolution. Think about it this way. Any living cell, regardless of the organism it is part of, is an incredibly intelligent, purpose driven entity. Every organ in the human body and every cell in the human body has specific purpose, kidneys remove toxins, hearts pump blood, brains control everything. Individual white blood cells fight invaders, others transport nutrients, and on and on. Why is it that we can accept cells do such incredible purpose driven things internally and externally, but yet we forbid them from editing their own DNA, an organ of the cell, to accomplish their tasks? It is so blindingly obvious at this point it beggars belief that people still adhere to the gene centric view.

Of course mutations happen, every cell is constantly using its DNA to build whatever is needed for its purpose. Trillions of cells in the human body, all madly at work to accomplish their tasks. Billions of transcriptions going on, and incredible error correction involved to ensure that any copying errors are corrected. All controlled by the cell itself, working on instructions from the organism, and not controlled by some dumb piece of inert molecule. DNA without a cell is inert, it is the cell that uses DNA, not the other way round. The coding portion of DNA is a toolkit, it controls nothing and does nothing, it just sits there and acts as a template for the cell to build whatever it needs, like lego, using the 80% of DNA that is mobile.

It is not reasonable to question that evolution occurs, but it is quite reasonable to question the mechanisms involved in evolution, this is what scientists have been doing for the past 150 years. Scientists 150 years from now will look back and think we were primitive. We should stop acting primitive, as if we know everything when we are still much closer to knowing nothing. What current science is telling us on the subject is that Darwin and Lamark were both right, and the neo-Darwinists are wrong, variation is due to both genuinely random processes and incredibly orchestrated processes in response to environmental pressure. Horizontal gene transfer is a dominant player in evolution as is epigenomics and both are clearly Lamarkian.

It may be time to launch the idea of a posthumous Nobel prize, Lamark would be a deserving first recipient.

nozzferrahhtoo

nagirrac wrote: »

The fact that identical genotypes gives rise to different phenotypes (in identical twins) i.e. organisms with different morphology and physiology, discredits the central dogma of evolution.

Ummm, no, no it doesn't.

I have studied biology and evolution for many a year now and I can not think of one single thing I have read that even suggests that identical twins should be expected to actually be identical. Quite the opposite in fact.

So I am entirely unsure what you are saying here. What "dogma" exactly is discredited by things like identical twins exactly?

robindch

nagirrac wrote: »

Just talking to myself here [...]

nagirrac - I've move your "discredits the central dogma of evolution" post, and the follow-up, from the evolutionary-science thread into this one where it belongs.

You might have more luck starting a discussion if you drop the pseudo-religious "dogma" claptrap and try to approach it from a scientific perspective via posts which clearly and succinctly describe a single, unambiguous point of view.

nagirrac

robindch wrote: »

You might have more luck starting a discussion if you drop the pseudo-religious "dogma" claptrap and try to approach it from a scientific perspective via posts which clearly and succinctly describe a single, unambiguous point of view.

Robin, the central dogma of evolutionary biology is not claptrap, nor pseudo-religious. It is taught in every molecular biology class, and features in every molecular biology textbook. It was first proposed by Francis Crick in 1958! Perhaps yourself and nozz should open those biology textbooks again and lay off the ad hominum. I am absolutely approaching this from a scientific standpoint, religion or belief in God is completely irrelevant.

http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/MolBioReview/central_dogma.html

You are perhaps confusing it with what I refer to as the dogma of militant atheists like Jerry Coyne, that is a separate issue. One worth discussing but not related to this topic. Here is Larry Moran on the central dogma of evolutionary biology:

http://sandwalk.blogspot.com/2007/01/central-dogma-of-molecular-biology.html

robindch

nagirrac wrote: »

Robin, the central dogma of evolutionary biology is not claptrap, nor pseudo-religious.

It may well be, but in a forum with heavy religious overtones, it's perhaps best to avoid religious terminology when discussing things that aren't religious.

Referring to it as the Central Dogma and provided a link to further info might help; as would avoiding unspecific references to teleology, heresy and other religious terms.

nozzferrahhtoo

nagirrac wrote: »

yourself and nozz should open those biology textbooks again and lay off the ad hominum.

Where is there any such thing in my post exactly?? Or are you just avoiding answering the actual post by imagining things in it that simply are not there?

Delirium

nagirrac, any chance you could maybe give a brief post on what this revolution is for us non-science nerd folk?

nagirrac

nozzferrahhtoo wrote: »

I have studied biology and evolution for many a year now and I can not think of one single thing I have read that even suggests that identical twins should be expected to actually be identical. Quite the opposite in fact.

So I am entirely unsure what you are saying here. What "dogma" exactly is discredited by things like identical twins exactly?

It sounds like you are as unfamiliar with the central dogma of evolutionary biology is so I recommend you read the articles I posted above. While Francis Crick first proposed the central dogma, it is the version that was described by Jim Watson that became the standard, and made its way into every biology textbook. So, for clarification, the "dogma" I am talking about is the central dogma described by Watson, as this is the one every undergrad in biology is taught.

The central dogma (Watson's) states that the pathway for the flow of information is DNA ---> RNA ---> through transcription and translation and that this is irreversible.

Identical twins develop from one zygote, so they have an identical genome.
This removes genetics from the equation as to why they develop separate traits during their lifetimes, and clearly shows that this is an exception to the central dogma rule (among many other exceptions like horizontal gene transfer, read Larry Moran's article). The mechanisms involved that explain the differences between identical twins as they age is epigenetics, which is influenced by environment (diet, exposure to toxins, whatever). Epigenetics involves proteins (specifically enzymes) adding tags to DNA which impacts gene expression, without changing the DNA sequence. So, in other words turning on or off genes independent of the processes described by the modern synthesis of which the central dogma is now a component.

You might want to also consider withdrawing your "I believe you are a layperson" jibe from the "other" forum, although I won't hold my breath.

nagirrac

robindch wrote: »

It may well be, but in a forum with heavy religious overtones, it's perhaps best to avoid religious terminology when discussing things that aren't religious.

Referring to it as the Central Dogma and provided a link to further info might help; as would avoiding unspecific references to teleology, heresy and other religious terms.

I will try and be more specific to avoid confusion. However, terms like dogma and teleology are not religious, although they can be interpreted as such.

Teleology holds that nature has a final cause or is purposeful. It has nothing to do with belief in God or religion, unless you believe that God is nature or God controls nature. Teleology is a philosophy not a religion.

Surely you accept that it is not just the religious who can be dogmatic?

Ziphius

A quick point as I haven't had time to read the linked article.

It is known as the central dogma of molecular biology not evolutionary biology. And was devised in the 1950s after the discover of the structure of DNA. The Modern Synthesis was developed earlier --in the 20s and 30s. So, the dogma is not, at least originally, part of the synthesis.

The dogma just explains the directional flow of information: from DNA to RNA to protein. Prior to this people were not sure where the genetic information was stored, many assumed that the genes where located in the histone proteins found in chromosomes and that the DNA merely held them together.

robindch

nagirrac wrote: »

[...] terms like dogma and teleology are not religious, although they can be interpreted as such [...]

As above, do bear in mind where you're posting -- around here, dogma and teleology are used primarily, and probably exclusively, in connection with religious arguments and arguments aren't made any cleared by using them in a non-religious discussion.

nagirrac

robindch wrote: »

As above, do bear in mind where you're posting -- around here, dogma and teleology are used primarily, and probably exclusively, in connection with religious arguments and arguments aren't made any cleared by using them in a non-religious discussion.

As this is a non religious discussion, what word do you suggest I use in the place of teleology to avoid confusion?

robindch

nagirrac wrote: »

As this is a non religious discussion, what word do you suggest I use in the place of teleology to avoid confusion?

"Goal oriented". Though you'll need to say what the goal is, at which point it's arguable a to whether even the substitute term actually contributes anything to the debate (probably not).

In general, sticking to concrete reality in prose that has one, unambiguous meaning produces best results around here.

nagirrac

koth wrote: »

nagirrac, any chance you could maybe give a brief post on what this revolution is for us non-science nerd folk?

I will give it my best shot koth, but as I am about to head off for the Thanksgiving break, I apologize if I cannot respond to follow up questions in a timely fashion. Hopefully this will generate a bit of discussion though.

The mechanism of biological evolution is stated almost exclusively as "random mutation followed by natural selection". You see it defined as such here on boards in almost every discussion that involves evolution.

The following is a summary of an article by James Shapiro, who is a Professor of Molecular Biology at the University of Chicago (the same place as Jerry Coyne coincidently).

Evolution is highly complex and cannot be reduced to simple formulas like RM:NS. It does not proceed by the kind of small incremental steps that one would expect from such a simple formula. The following are some known mechanisms that are not RM:NS and are a much better explanation of why evolution results in novel features, sometimes rapidly and sometimes very abruptly.

Horizontal gene transfer is the most well known. Vertical gene transfer is what most people are familiar with, the transfer of genes from parent to offspring through reproduction. HGT proceeds by several different mechanisms and is firmly established in the scientific community, it is the basis for artificial genetic engineering. One of the impacts of HGT is that the whole idea of the "tree of life" has come into question. Carl Woese, arguably the greatest microbiologist of the 20th century, argues against common descent and that under extreme conditions of HGT, there is no tree of life.

The best example of HGT is the development of antibiotic resistant bacteria. This has absolutely nothing to do with the simple RM:NS model, it is entirely due to horizontal gene transfer, which is what makes it so dangerous due to its rapid evolution.

The second important source of evolutionary novelty is cell mergers (endosymbiosis) and co-evolution. This is seen everywhere in nature, 90% of the cells in humans are bacteria and viruses, and almost all are beneficial.

Epigenetics is the most recent development and involves changes to the epigenome (which surrounds the genome), due to the environment the organism is exposed to. Up to recently these changes were believe to not be hereditary, but there is now significant data in the recent 5 - 7 years that show some epigenetic changes are passed down for several generations. So, for example, if you smoke cigarettes and this causes changes to your epigenome which in turn causes harmful effects to your DNA, this can be passed down to your grandchildren.

The important common feature of all of the above is that they are cell driven mechanisms rather than DNA driven. The cell is in charge, not an inert molecule like DNA. There is a great animation in youtube which I will try and find again, it shows how cells operate from inside the cell and is breathtaking. Everything that the cell does has purpose.

Arguably the most important thing that cells do is actively repair and restructure their genomes, for example fixing copying errors, or fixing mutations caused by the environment. The cell restructures its own DNA, in response to environmental stress, this is what Shapiro refers to as "Natural Genetic Engineering".

Why would we be surprised at this? We are doing genetic engineering ourselves now, which we learned like everything we have learned from studying nature. Nature is simply much smarter than we are, we should give it the respect it deserves, and stop describing it in terms of dumb, mindless processes.

Delirium

Thanks for that and enjoy Thanksgiving break:)

nagirrac

Specifically on identical twins, this is a good summary of epigenetic effects. Of particular note is the % contribution from epigenetics versus genetics for diseases like MS, RA, breast cancer, Crohn's disease, and stroke.


http://learn.genetics.utah.edu/content/epigenetics/twins/

nozzferrahhtoo

nagirrac wrote: »

It sounds like you are as unfamiliar with the central dogma of evolutionary biology is so I recommend you read the articles I posted above.

I am more familiar with the subject than you appear to be. And my question stands unanswered by the post you have just made.

Once again: I am aware of no aspect of Evolutionary Biology that suggests that Genetically Identical twins should actually be in identical. Quite the opposite.

So I am entirely unaware what aspect of biology you feel is contradicted by identical twins having different morphology and physiology.

This fact about identical twins in no way contradicts anything I know or have learned about Biology or Evolution. Yet you claim it does.

So I am all ears to hear how.

nagirrac wrote: »

You might want to also consider

I consider everything I write, and write it for a reason.

YOU might want to consider simply writing your own posts, minding your own business, and leaving me to write mine. You input could not be less relevant to how I choose to write my own posts thanks, so stow it.

El_Duderino 09

nagirrac wrote: »

Nature is simply much smarter than we are, we should give it the respect it deserves, and stop describing it in terms of dumb, mindless processes.

Thanks for that Nagirrac. It was really interesting. I suppose on this forum evolution is often discussed within the context of explaining it to people who have a strawman understanding of evolution. For that reason RM:NS is a good starting point.

I'm delighted that our understanding of evolution is growing and can cause a feeling of wonder as we struggle to take in the scale of the process.
However this is no excuse for anthropomorphising nature in the way you have in the last paragraph. Maybe you were doing it for effect. The time to stop describing a process as mindless is when we have evidence for it possessing a mind.

nozzferrahhtoo

But a mindless process it is.

While some of nagirracs posts do successfully point out that there is a lot more to evolution than many lay people think, and the results are much more complex than we can sometimes fathom, none of this in any way suggests evolution is anything but a simple mindless process that gives complex and awe inspiring results.

Alas what too many people do is view the results of evolution, such as the massive interdependence and interconnections of the workings of the human cell, and simply assert off the basis of nothing but their own incredulity, that these results could not have come from a simple mindless process, and some kind of mind and/or design must be involved.

And it is precisely at that point that the discourse between Creationists and Evolutionary Scientists all too often breaks down.

nagirrac

El_Duderino 09 wrote: »

I'm delighted that our understanding of evolution is growing and can cause a feeling of wonder as we struggle to take in the scale of the process. However this is no excuse for anthropomorphising nature in the way you have in the last paragraph. Maybe you were doing it for effect. The time to stop describing a process as mindless is when we have evidence for it possessing a mind.

I assure you it's not for effect, its simply a philosophical statement that is supported by the evidence, although it does not reach the level of a scientific theory. The evidence is that nature has developed minds to the degree that they are self-aware, by some mechanisms we understand, and some of which we don't understand and may never understand. Concluding that nature is blind and purposeless is the height of primate arrogance, given we have no idea what nature may have developed elsewhere in the universe or may develop.

One of my frustrations with threads that discuss evolution, here and elsewhere, is the concept that there are atheists and creationists and nothing in between, a position of utter ignorance and narrow mindedness. While its somewhat understandable among those with a rudimentary grasp (or none) of evolution, it is unforgivable in my opinion when some of the more militant atheists like Jerry Coyne and to a lesser extent Richard Dawkins, attack fellow scientists who dare question any aspect of the established theory of evolution, as if it were scripture, and label them as ID proponents. As an example one of their targets is Paul Davies (not just a most excellent scientist in several disciplines, but also broadly versed in philosophy), even though Davies wrote possibly the best rebuttal of ID ever written in the "The Goldilocks Enigma".

Darwin's theory (or rather theories of evolution) is one of the broadest in science, with the result that as science unfolds and new discoveries are made, they fit with his original concepts. There is nothing wrong with RM:NS, it helped us enormously in understanding how evolution proceeds, along with the numerous other mechanisms discovered since the 1930s. The latest discoveries in epigenetics make my above point (the modern definition which refers to "inheritance of acquired traits due to changes to DNA but not involving changes to DNA sequence", rather than the older view which simply meant development). Regardless of the opposition from Coyne and others epigenetic inheritance will be incorporated into the theory of Evolution and on we go, onward and upward as always in science.

The important thing is never to let dogma stand in our way, whatever its source. Our ancestors will look back on us and regard us as ignorant, just like we regard many of the ideas from prior centuries. We are confronted with many enigmas and paradoxes in trying to explore and explain the universe we find ourselves in, and pretending we know everything there is to know on any subject is not going to advance our knowledge.

Sorry for the rant, only the first paragraph is in response to your post.

El_Duderino 09

nagirrac wrote: »

I assure you it's not for effect, its simply a philosophical statement that is supported by the evidence, although it does not reach the level of a scientific theory. The evidence is that nature has developed minds to the degree that they are self-aware, by some mechanisms we understand, and some of which we don't understand and may never understand. Concluding that nature is blind and purposeless is the height of primate arrogance, given we have no idea what nature may have developed elsewhere in the universe or may develop.

One of my frustrations with threads that discuss evolution, here and elsewhere, is the concept that there are atheists and creationists and nothing in between, a position of utter ignorance and narrow mindedness. While its somewhat understandable among those with a rudimentary grasp (or none) of evolution, it is unforgivable in my opinion when some of the more militant atheists like Jerry Coyne and to a lesser extent Richard Dawkins, attack fellow scientists who dare question any aspect of the established theory of evolution, as if it were scripture, and label them as ID proponents. As an example one of their targets is Paul Davies (not just a most excellent scientist in several disciplines, but also broadly versed in philosophy), even though Davies wrote possibly the best rebuttal of ID ever written in the "The Goldilocks Enigma".

Darwin's theory (or rather theories of evolution) is one of the broadest in science, with the result that as science unfolds and new discoveries are made, they fit with his original concepts. There is nothing wrong with RM:NS, it helped us enormously in understanding how evolution proceeds, along with the numerous other mechanisms discovered since the 1930s. The latest discoveries in epigenetics make my above point (the modern definition which refers to "inheritance of acquired traits due to changes to DNA but not involving changes to DNA sequence", rather than the older view which simply meant development). Regardless of the opposition from Coyne and others epigenetic inheritance will be incorporated into the theory of Evolution and on we go, onward and upward as always in science.

The important thing is never to let dogma stand in our way, whatever its source. Our ancestors will look back on us and regard us as ignorant, just like we regard many of the ideas from prior centuries. We are confronted with many enigmas and paradoxes in trying to explore and explain the universe we find ourselves in, and pretending we know everything there is to know on any subject is not going to advance our knowledge.

Sorry for the rant, only the first paragraph is in response to your post.

You know it might be a problem with me but I find it hard to agree with you even when I mostly agree with the main point you're making. I think when it comes to argument you prefer confrontation to constructive dialectic.

If you are surprised that ideas discussed in this forum tend to have a religious component, then I don't know what to tell you. Have you considered the Science forum for a more purely scientific discussion?

Yes we don't know everything about nature. Yes, as long as you acknowledge that its not at the level of hypothesis then you can say whatever you like. Conscious mindful nature, mindful televisions, mindful house, mindful rocks. Have you considered the Spirituality or Philosophy fora for these ideas?

Just because we don't have evidence for an idea doesn't mean we should shun those who think about it. However we should not pretend that 'mindful nature hypothesis' should be included in every conversation about evolution until it has actual evidence behind it. I'm sure you know that.

When it comes to discussing how things work, it's right to discriminate in favour of theories with the most favourable balance of evidence.

recedite

nagirrac wrote: »

Any living cell, regardless of the organism it is part of, is an incredibly intelligent, purpose driven entity.

I've just been talking to my skin cells. Not getting much response.

robindch

nagirrac wrote: »

We are confronted with many enigmas and paradoxes in trying to explore and explain the universe we find ourselves in, and pretending we know everything there is to know on any subject is not going to advance our knowledge.

I hadn't realized that anybody -- other than certain amongst the religious -- do believe they have access to infinite knowledge.

nagirrac wrote: »

Sorry for the rant [...]

Apologies accepted!

nagirrac

El_Duderino 09 wrote: »

I think when it comes to argument you prefer confrontation to constructive dialectic. If you are surprised that ideas discussed in this forum tend to have a religious component, then I don't know what to tell you. Have you considered the Science forum for a more purely scientific discussion?

Yes we don't know everything about nature. Yes, as long as you acknowledge that its not at the level of hypothesis then you can say whatever you like.

Yes, I freely admit to being confrontational when it comes to arguments regarding science and religion, and in that regard I feel quite at home here in A&A:). Confronting ideas is a good thing, most atheists on this forum and others are confrontational towards believers, and reasonably so, but there's also nothing wrong with believers confronting atheists. Especially when making claims that have are unsupportable, like there is nothing good that comes from religion (I am not saying you make this claim).

I never make any claim without evidence, although there are some who would claim otherwise (while providing no evidence of this themselves). If by hypothesis you mean scientific hypothesis, this is defined as a proposed explanation for some aspect of nature that is testable. The God hypothesis for example does not rise to the level of a scientific hypothesis in my view as it is untestable. However, arguments for the "mindfulness" of nature or of cells for example is a scientific hypothesis and is testable. The fact that most people don't believe it is irrelevant, most people believed at one point that the sun revolved around the earth, or that the earth was flat, as the evidence available at that time supported that view.

Before either advocating or denying that nature is mindful, we need to define what we mean by mind. A tough one to pin down, but I would say anything that makes deliberate choices from available options is mindful. A simple example is whether the underlying mechanisms of biological evolution are random or adaptive. If solely random, then clearly there is no "mind" involved. Most scientists and laypeople would say random. However, it is increasingly very difficult nowadays to get two biologists to agree on a common definition of "random", and most laypersons misunderstand the term completely. The most correct definition in my opinion is that the outcome of an evolutionary mechanism (random mutation, genetic drift, lateral gene transfer, or whatever) bears no relation to the likelihood of the mechanism happening e.g. mutations happen at a certain rate or frequency, and over long periods those that are beneficial are selected and lead to variation within populations and eventually to speciation. In other words natural selection "designs" organisms by working on accidents of nature.

The central argument of Shapiro, which is scientific, and which I agree with, is that genome change leading to evolutionary change is not caused by a series of accidents but caused by regulated processes of the cell. The attached article by Shapiro summarizes the major points of his hypothesis. I am sure I will be accused again of not writing my own posts, which is ironic given the same posters demand independent evidence for any claim (as they should).

http://shapiro.bsd.uchicago.edu/Shapiro.1997.BostonReview1997.ThirdWay.pdf

nagirrac

recedite wrote: »

I've just been talking to my skin cells. Not getting much response.

They don't speak English:D

nagirrac

robindch wrote: »

I hadn't realized that anybody -- other than certain amongst the religious -- do believe they have access to infinite knowledge.

That's not my claim robin. My claim is that militant atheists and creationists are both guilty of stifling open-minded discussion regarding ongoing discoveries in biological evolution. A "dialog of the deaf" so to speak.

nozzferrahhtoo

nagirrac wrote: »

I assure you it's not for effect, its simply a philosophical statement that is supported by the evidence, although it does not reach the level of a scientific theory.

If you think Evolution as a guided process is anything more than waffle based on artistic license for effect, then I am all ears to hear how exactly this is "supported by the evidence". So far you have not presented any while asserting existence of same. All I am really seeing from your OP posts for example is a verbose version of "It is all so complicated, therefore design" style thinking.

nagirrac wrote: »

The evidence is that nature has developed minds to the degree that they are self-aware

That would be the "Fallacy of Composition" right there. Just because evolution/nature has produced intelligent, conscious, designing minds.... this in no way licenses us to declare Evolution and/or nature to itself by intelligence, conscious, or designing.

nagirrac wrote: »

Concluding that nature is blind and purposeless is the height of primate arrogance

But concluding that there is not a shred of argument, evidence, data or reasoning on offer (much less so from you) to suggest it is anything but a mindless, purposeless, blind process is perfectly ok.... because that is the facts it seems.

nagirrac wrote: »

One of my frustrations with threads that discuss evolution, here and elsewhere, is the concept that there are atheists and creationists and nothing in between

I am not seeing anyone asserting that. So your frustrations seem to be directed at your own imagination it seems. In fact quite a few, if not the vast majority, of well informed atheists are perfectly aware that we owe our thanks, for example in the Dover trial, to people like Devout Catholic Kenneth Miller, for our victories against the vocal lawyer toting minority that is American Creationism.

But you seem to be deflecting again now with your own self confessed rant. Threads with you on them seem to derail from your unsubstantiated points quite quickly in favor of you discussing people who you imagine annoy you. Often people who are not even posting on the thread thus derailed or may not even exist outside your own head.

The question people are trying to pin you down on is what basis you have for suggesting nature and/or evolution is anything but a mindless blind process which gives the illusion of design or goals quite well but no reason to actually think that anything BUT an illusion.

You yourself use the specific definition of "Deliberate Choices" and I am agog to see where nature made any "Deliberate" choice in our evolutionary history.

Ziphius

I've just read the paper (more or less). And there is plenty I disagree with, yet I don't see how you can conclude from Noble's arguments that organisms and cells (!) are self aware and intentionally evolving towards a specific goal.

sea_monkey

Most of the research being done with regards to how genetic information is passed on is to do with ncRNA. (DNA which isnt translated into proteins)

http://hmg.oxfordjournals.org/content/15/suppl_1/R17.long

Basically saying that Alleles are no longer the only method through which traits can be passed
can cause things such as http://en.wikipedia.org/wiki/Prader%E2%80%93Willi_syndrome


its still caused by mutations and shifts in the genome though so i wouldnt discredit the central dogma at all.

If every thing went right and nothing changed then thats exactly what would happen, then agin if everything went right we wouldnt be here.

gaynorvader

What is the "central dogma" of evolution?

Ziphius

gaynorvader wrote: »

What is the "central dogma" of evolution?

There isn't one. The "central dogma" refers to molecular biology.

Put simply, genetic information is stored in DNA which is translated into RNA and the RNA codes for proteins.

http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology

nagirrac

Ziphius wrote: »

I've just read the paper (more or less). And there is plenty I disagree with, yet I don't see how you can conclude from Noble's arguments that organisms and cells (!) are self aware and intentionally evolving towards a specific goal.

My conclusions, which you misstate, are not from Noble's arguments, they are from Shapiro's arguments. Noble in the first paper I presented summarizes the current challenges to the neo-Darwinian Modern Synthesis, and is basically making the argument that a new modern synthesis is long overdue. Noble references Shapiro throughout his paper, the full extent of Shapiro's arguments are in the paper attached to post 28 above.

I haven't used the phrases "self aware" nor "evolving toward a specific goal" so not sure why you are attributing these beliefs to me. Whether nature is teleological, as these claims would imply, is an open question that we have about as much evidence to support or refute as Krauss' "Universe from Nothing" i.e. none. "Mindful", a word I have used, does not imply self awareness. For example, our brains monitor billions of cells in our bodies every second and make decisions, without our being aware of it. We are "self aware" of very little that goes on biologically in our bodies, so we have to conclude life by and large does not need self awareness.

What Shapiro is arguing is that we should not submit to the ideology that evolution progressed only by random accidents, in particular when our knowledge of the genome is still in its infancy. In doing so he of course gets accused by militant atheists of being an ID proponent, as of course is everyone who dares to question neo-Darwinism. The only valid scientific discussion is whether Shapiro's Natural Genetic Engineering hypothesis has validity. Furthermore, in referencing Shapiro, militant atheists always bring God into the discussion. In fact one of Shapiro's most active critics, Larry Moran, finished his review of Shapiro's recent book with the supreme "aha" moment.. "I once asked Shapiro if he believed in God, and he refused to answer". What Larry forgets is that the question of belief in God or lack of belief in God is and should be irrelevant to science, unless of course the militant atheist real agenda is to drive all religious people out of science.

Asking the question is there intelligence involved in evolutionary processes is not the same as claiming there is intelligence involved in evolutionary processes. Questioning the mechanisms of evolution is not the same as questioning evolution itself. The hostility shown towards Shapiro and other scientists (and these are true scientists) has the same origins as that which resulted in Barbara McClintock, a brilliant scientist, ceasing publishing her work in 1953 due to the abuse directed her way from fellow scientists. She was later awarded a Nobel prize for her work, 30 years later, when most of those that had abused her were long dead.

nagirrac

Ziphius wrote: »

Put simply, genetic information is stored in DNA which is translated into RNA and the RNA codes for proteins.

http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology[/QUOTE]

Open to correction, but that's not the Central Dogma, or rather is the less controversial aspect of the Central Dogma. The Central Dogma, as outlined by Watson in 1970, and taught to biology students ever since, is that the information flow you outlined is irreversible. This has been shown to be false, by several cellular processes (referenced later in the wiki article), the most recent being epigenetics, where proteins can and do impact gene expression, and the changes in gene expression are inherited.

It was an unfortunate choice of wording by Crick originally, but one that was made much worse later by Watson, after which it essentially became dogma.

Ziphius

nagirrac wrote: »

I haven't used the phrases "self aware" nor "evolving toward a specific goal" so not sure why you are attributing these beliefs to me.

You have, however, used these words;

"Any living cell, regardless of the organism it is part of, is an incredibly intelligent, purpose driven entity."

and:

"The conclusions of Shapiro's work is that all organisms are sentient,
are intrinsically teleological (tending towards a goal), and nature acts like a genetic engineer."

So, you can understand my confusion.

Can you state clearly and concisely what, exactly, your problem with the modern synthesis and your support for this conclusion.

Ziphius

nagirrac wrote: »

Open to correction, but that's not the Central Dogma, or rather is the less controversial aspect of the Central Dogma. The Central Dogma, as outlined by Watson in 1970, and taught to biology students ever since, is that the information flow you outlined is irreversible. This has been shown to be false, by several cellular processes (referenced later in the wiki article), the most recent being epigenetics, where proteins can and do impact gene expression, and the changes in gene expression are inherited.

It was an unfortunate choice of wording by Crick originally, but one that was made much worse later by Watson, after which it essentially became dogma.

In fairness, I did say 'put simply'. But yes, the central dogma does state that the direction of information goes from DNA to proteins and not the other way round.

TBH, I don't think epigentics challenges this. Sure, there a factors which alter the expression of genes but are there any cases were a protein codes for a gene. Is the information flow from DNA to RNA to Protein ever reversed? That would certainly be interesting.

Ziphius

nagirrac wrote: »

My conclusions, which you misstate, are not from Noble's arguments, they are from Shapiro's arguments. Noble in the first paper I presented summarizes the current challenges to the neo-Darwinian Modern Synthesis, and is basically making the argument that a new modern synthesis is long overdue. Noble references Shapiro throughout his paper, the full extent of Shapiro's arguments are in the paper attached to post 28 above.

Apologies, I missed the second paper. I will have a look when I have more time.

nagirrac

Ziphius wrote: »

So, you can understand my confusion.

Can you state clearly and concisely what, exactly, your problem with the modern synthesis and your support for this conclusion.

The confusion is between a scientific hypothesis or theory, and a philosophical conclusion. Two individuals looking at the same scientific evidence, one who believes there is intelligence behind the universe as we observe it, and the other concluding there isn't. The view that only the latter philosophical position is valid is the arrogant view of the militant atheist.

From a scientific standpoint my problem with the modern synthesis is that it is incomplete and out of date. The question simply stated is do we need to add components to our evolutionary theory, and the answer is yes. The only people who argue against this are those who believe the modern synthesis as it stands explains everything there is to know about evolution.

The main problem with the modern synthesis is that it left developmental biology out of the picture, something that is now being addressed by the field of Evo-Devo. Saying that "everything has been explained" is not a good response to naturally occurring phenomena that are currently difficult to explain. What current science is telling us is that there are many layers of heritable variation, above and beyond the gene-centric one, facilitated variation, phenotypic plasticity and epigenetic mechanisms.

So, your challenge to me is how can I can arrive at a philosophical conclusion from all of the above evidence that nature is intelligent and purpose driven? Quite easily, in exactly the same manner as someone who concludes the opposite i.e. that nature is blind and directionless. In fact I used to subscribe to the latter position, until a careful review of all of the evidence from all sources has convinced me otherwise. If you were to ask me to cite a single piece of evidence from biology, then I would say phenotypic plasticity (how different phenotypes evolve from the same genotype due to their changing environment) and the role of epigenetic inheritance.

sea_monkey

Proteins can and do alter gene expression yes but to say the dogma is reversible is wrong. They act as activators for gene transcription and defects can cause major changes to how how genes are expressed (p53 defects in 50% of cancers)

you wont see a protein go through a ribosome, come out as mRNA have introns re-added then get reverse transcribed into DNA.
Differences in ncRNA is what can cause epigentic inheritance, this is what goes against the dogma.

it was previously believed that the 98% of DNA which didnt code for proteins was junk but now its known that 70% or more of the DNA is transcribed and has regulatory functions in the form of ncRNA. Its when this RNA has an adverse effect on normal DNA transcription that you can get mutations and genetic drift. so the dogma is looking something like this.
DNA+activator proteins -> RNA +ncRNA -> mRNA+ncRNA->alternative splicing ->proteins


The flow of information in relation to protein coding genes is still DNA->RNA->Proteins

recedite

Interesting article I read in today's London Times concerning epigenetics in mice. In the full article, it mentioned the name of the particular molecule or compound which formed the characteristic smell of a food. The food was accompanied by shock treatment. Offspring of the mice had extra receptors for the chemical, and showed aversion to it, despite never having received the shock themselves.

What all this shows is that the scientific method is open to enquiry and does not have a rigid dogma. Even Darwin would probably have said his theory was just a foundation.
But nowhere does it indicate cells acting with their own intelligence and purpose.
BTW isn't it funny how they only give you a choice between the Indo and The Times in Mc Donalds

Ziphius

recedite wrote: »

Interesting article I read in today's London Times concerning epigenetics in mice. In the full article, it mentioned the name of the particular molecule or compound which formed the characteristic smell of a food. The food was accompanied by shock treatment. Offspring of the mice had extra receptors for the chemical, and showed aversion to it, despite never having received the shock themselves.

What all this shows is that the scientific method is open to enquiry and does not have a rigid dogma. Even Darwin would probably have said his theory was just a foundation.
But nowhere does it indicate cells acting with their own intelligence and purpose.
BTW isn't it funny how they only give you a choice between the Indo and The Times in Mc Donalds

Story is in New Scientist too for those interested.

http://www.newscientist.com/article/dn24677-fear-of-a-smell-can-be-passed-down-several-generations.html#.Up0NPsRDuSo

robindch

nagirrac wrote: »

[...] the militant atheist [...]

As above, I you'd have far more success igniting some interest in this topic if you could avoid, as El_Duderino pointed out above, unnecessary name-calling like this -- it really has no part in this debate and frankly, it's quite tiresome to have to keep pointing this out to you.

Mark Hamill

nagirrac wrote: »

Two individuals looking at the same scientific evidence, one who believes there is intelligence behind the universe as we observe it, and the other concluding there isn't. The view that only the latter philosophical position is valid is the arrogant view of the militant atheist.

What makes the latter view arrogant and militant, but yours not? As you say yourself, you use the same methods to arrive at your conclusions as they do:

nagirrac wrote: »

So, your challenge to me is how can I can arrive at a philosophical conclusion from all of the above evidence that nature is intelligent and purpose driven? Quite easily, in exactly the same manner as someone who concludes the opposite i.e. that nature is blind and directionless.

so you must be equally arrogant and militant.

nagirrac wrote: »

In fact I used to subscribe to the latter position, until a careful review of all of the evidence from all sources has convinced me otherwise. If you were to ask me to cite a single piece of evidence from biology, then I would say phenotypic plasticity (how different phenotypes evolve from the same genotype due to their changing environment) and the role of epigenetic inheritance.

And, briefly, what aspects of phenotypic plasticity and epigenetic inheritance make them appear intelligently driven to you?

nagirrac

Mark Hamill wrote: »

What makes the latter view arrogant and militant, but yours not? As you say yourself, you use the same methods to arrive at your conclusions as they do:

so you must be equally arrogant and militant.

The word only in the sentence, "the view that only the latter philosophical view is valid..". As a former atheist I find both positions valid, that is the difference which some seem to spectacularly miss.

nagirrac

robindch wrote: »

As above, I you'd have far more success igniting some interest in this topic if you could avoid, as El_Duderino pointed out above, unnecessary name-calling like this -- it really has no part in this debate and frankly, it's quite tiresome to have to keep pointing this out to you.

I didn't invent the term "militant atheist" robin and it is quite commonly used in popular culture. It is not an attack on the person, it is an attack on their beliefs;), and considerably milder than calling people delusional, or suffering from mental illness as happens all too frequently towards religious believers.

It is also not a derogatory term, the proper understanding of the term militant in this context is "someone who has combative and aggressive support for a cause", in this case the cause being to rid the world of religion. Dawkins himself, who is much milder than Jerry Coyne, has stated his disappointment that the goal will not happen in his lifetime. I happen to disagree, also in a combative and aggressive manner, which I suppose means I am a militant deist (and there are far fewer of us than militant atheists).

By no means do I think all atheists, or even most atheists, are militant atheists. Although many New Atheists influenced by the likes of Dawkins appear to be.

nagirrac

Mark Hamill wrote: »

And, briefly, what aspects of phenotypic plasticity and epigenetic inheritance make them appear intelligently driven to you?

Right, getting back on topic.

Firstly, how do we define intelligence? If we start with the wiki definition, generally a good starting point: "Intelligence has been defined in many different ways, including logic, abstract thought, understanding, self-awareness, emotional knowledge, communication, learning, retaining, planning and problem solving".

I would say cells exhibit several of these traits. There are also many of these traits where we cannot say today with any level of confidence that cells exhibit, mostly because we have no way of knowing presently. We know that cells communicate and are able to solve problems (e.g. error correction). There is now strong indication that they retain information by adapting to their environment and passing on the adaptation to their offspring (epigenetics). Not necessarily in a willful way but in an adaptive way, especially in a highly stressed environment. Like mutation this can have a positive or negative impact in terms of survival, but more important is the link to novel features. Up to recently, random point mutation of DNA has been regarded as the primary provider of variability for natural selection to do its work, resulting in the incredible diversity of life and the novel features that have evolved in so many species. An adaptive mechanism as outlined by sea-monkey above (if I understand it correctly) appears a very valid alternative, especially to explain rapid evolution as we see in multiple research papers in recent years. In other words is epigenetics the elusive "missing link" that explains the variation in phenotypes available to selection.

I struggle to see today why some people find the idea of intelligence in nature offensive. Is it the connection to God or a specific religious view that creationists insist on? Must everyone who sees intelligence in nature be labeled a creationist? Should science not pursue the idea of nature being intelligent lest it give fodder to creationists?

What are attempts to develop artificial intelligence other than attempts to duplicate what nature has done in terms of developing intelligent traits?

nozzferrahhtoo

gaynorvader wrote: »

What is the "central dogma" of evolution?

There is none really. It is just religious linguistics being used, despite the moderators asking it not be, in order to attempt to rile up a reaction in people.

The only central fixed point I know of in Evolution is that it happened. Evolution is a fact.

The rest.... The Theory Of Evolution.... is our ruminations on how it went about happening and why.

The difference between a fact (Such as Gravity exists) and a Theory (The Theory of Gravity) is stark but willfully ignored by many.

Other than that I can think of no central fixed point in Evolution and the OP appears to be reacting against things that are not actually there while outright ignoring things, like posts on this thread, that actually are there.

nozzferrahhtoo

nagirrac wrote: »

I would say cells exhibit several of these traits.

I see them exhibiting as many of these traits as I see replies from you to my last post on this thread. That is to say: None.

Let us go through your list however.

nagirrac wrote: »

logic

Cells do not exhibit logic. They merely conform to the "logic" that our universe constrains upon them. Cells exhibit "logic" just about as much as the rocks in my garden do therefore.

nagirrac wrote: »

abstract thought

Cells do not have a mind. They do not think. They do not plan. They do not engage in the production of art. Where exactly do we see Abstract thought in the cells?

nagirrac wrote: »

understanding

What do they "understand" exactly? They are just mindless machines like the one that puts wrapping on your mars bar. Cells exhibit no "understanding" of their own that I am aware of.

nagirrac wrote: »

self-awareness

Do you think cells are self aware then? Really?

nagirrac wrote: »

emotional knowledge

You will have to adumbrate what you even think this means, let alone how you think cells display it.

nagirrac wrote: »

communication

They do not, in the sense humans mean it, communicate. Not directly, and only in the loosest sense of the word indirectly. They respond to their environment but this is not "communication" per se.

It is like "flocking" in birds that dance a pretty pattern in the sky. They do complex turns and dips and dives, all as a group, and it looks.... fantastic. People often wonder how they "communicate" their intentions and achieve this.

But they do no such thing. They merely respond individually to nothing more than what their direct neighbour is doing. And that simply condition/setting is enough to send out a complex pattern throughout the whole flock. There is no "communication" here per se, except as I said in the very loosest terms of the word. Certainly no where even close to enough to justify the application of "intelligence" you are so desperately trying to smuggle into the thread.

nagirrac wrote: »

learning, retaining, planning, problem solving

Again they appear to do no such thing as above. But again I am all ears.

I can genuinely see how Evolution gives the illusion of design, a plan, a goal or even an intelligence. But an illusion it very much seems to be.

nagirrac wrote: »

I struggle to see today why some people find the idea of intelligence in nature offensive.

I find it unsubstantiated. Any impression you have of offense would appear to exist in your own head. But quite often on threads like this people all too willfully miscontrue simply disagreement with offense or attack.

I disagree with your position because it is unsubstantiated. Any attempt to misconstrue that by inventing emotional biases or agendas is just an obfuscation attempt.

Mark Hamill

nagirrac wrote: »

The word only in the sentence, "the view that only the latter philosophical view is valid..". As a former atheist I find both positions valid, that is the difference which some seem to spectacularly miss.

The views are contradictory, only one of them can be valid.

sea_monkey

I wouldn't go so far as to say epigenics is a result of a cell being sentient. That would assume that cells are capable of making their own decisions. Could you imagine if a load of your brain cells woke up in a bad mood and didnt want to go to work one day? eek!

The main driver of evolution is mobile genetic elements and exon copying/shuffling leading to selected traits.

Also, I'm confused. Is this a religious debate? If so, why? Can I pray really hard and get some sweet epigenetic traits?