"The Origin of Specious Nonsense"

Frank Bullitt · 09-02-2013 08:17PM

This might have a little relevance to this thread, interesting and a good watch.

Ziphius · 09-02-2013 08:38PM

nagirrac wrote: »

The initial results published by the ENCODE team has been vigerously debated in scientific and non scientific circles. Some of the attacks on the researchers are incredible, given the scope of the project and the fact that the scientists are just reporting their results and not drawing any conclusions as yet. The problem for many scientists and especially non scientists is that the results suggest intelligent design causation rather than random causation so of course they must be wrong. I don't think we have ever seen such an example of anti-science hysteria in action, perhaps since Gallileo's time.

Have you any examples of this? Nothing I have read or listened to regarding the ENCODE project has mentioned any creationist or ID interpretations of the results. Though perhaps I haven't been following it closely enough.

darjeeling · 09-02-2013 08:49PM

nagirrac wrote: »

A bit surprising nobody has mentioned the ENCODE project as yet. This is the largest research project ever undertaking in science with hundereds of scientists working in collaboration across several countries. Although the project is ongoing a major update was released in late 2012 and the results are fascinating.

At the time the human genome was first decoded a decade ago scientists were surprised to find that only 1.5% of human DNA was involved in coding. The remaining 98.5% was referred to as "junk" DNA. This was perfectly in keeping with the new-Darwinian model of evolution being a messy process with random mutation leading to a fragmented DNA structutre with only a small % actually functional. Evolutionary biologists such as Dawkins have argued that the presence of so such junk DNA is validation for random mutation as the primary mechanism that drives natural selection.

The ENCODE project has looked at the functionality of DNA in a variety of human cells. The tentative conclusions are that 80% of DNA is biologically active and involved in regulation within human cells. It is regulation that turns genes on and off, for example leading to one type of cell becoming a brain cell and another a skin cell. The study has only looked at 147 types of cells so far and as the human body has thousands of different types of cells, there are strong reasons to suggest that the 80% number wll rise to 100% after further research.

The initial results published by the ENCODE team has been vigerously debated in scientific and non scientific circles. Some of the attacks on the researchers are incredible, given the scope of the project and the fact that the scientists are just reporting their results and not drawing any conclusions as yet. The problem for many scientists and especially non scientists is that the results suggest intelligent design causation rather than random causation so of course they must be wrong. I don't think we have ever seen such an example of anti-science hysteria in action, perhaps since Gallileo's time.

The next 5 years will be fascinating as the ENCODE project proceeds and evolutionary biologists fit the results into evolutionary models. We could well be on the cusp of another major breakthrough in our understanding of how evolution progresses.

The 80% figure has indeed been the subject of much debate - amongst scientists, many of whom have been highly critical. Essentially the 80% includes every bit of DNA that was transcribed into RNA. However, a lot of this transcription seems to be background noise, with the DNA being transcribed at very low levels in an unregulated fashion and having no evident functional role.

The idea that all of genomes could turn out to be functional doesn't seem to square with the long-established lack of correlation between genome size and organism complexity. Fugu fish, for instance, have a very small genome due in part to a very low level of transposable element 'junk' dna (2% of the genome vs 44% for humans).

In subsequent interviews, ENCODE project leader Ewan Birney has qualified the headline 80% figure, saying that he thinks that around 20% of the human genome may turn out to be functional.

This nature blog describes the controversy and explains the 80% vs 20% discrepancy.

nagirrac · 09-02-2013 09:09PM

Ziphius wrote: »

Have you any examples of this? Nothing I have read or listened to regarding the ENCODE project has mentioned any creationist or ID interpretations of the results. Though perhaps I haven't been following it closely enough.

It is too soon to make any firm conclusions as the data is so new and incomplete. However, what we can say I believe with some certainty is the concept of "junk" DNA has now to be discarded. Instead of being a messy, chaotic genome it now looks like we have what could be an incredibly functional genome (with some negatives of course like disease, but these are mainly due to errors in regulation processes and not in the genes themselves). The level of information transfer and complexity that is being discovered in the cell is virtually incompehensible. I am not stating that the ENCODE data proves anything, but it will in time lead to new understandings of the mechanisms of evolution as our understanding of how the genome works is now being completely updated..

We need to distinguish between creationists and those who consider intelligent design. Creationists believe in a speicfic "story" of creation as outlined in their religious texts. However, there are many who consider intelligent design who are not religious. If for example we eventually conclude that life as we know it on earth was desiged as opposed to having emerged from random processes, one obvious source is that life was designed elsewhere in the universe and either carried here by interstellar debris early in earth's history or brought to earth by an advanced alien civilization. There was certainly time for this to occur as the universe was around for 10 billion years before our planet formed.

mickrock · 09-02-2013 09:34PM

nagirrac wrote: »

However, there are many who consider intelligent design who are not religious. If for example we eventually conclude that life as we know it on earth was desiged as opposed to having emerged from random processes, one obvious source is that life was designed elsewhere in the universe and either carried here by interstellar debris early in earth's history or brought to earth by an advanced alien civilization. There was certainly time for this to occur as the universe was around for 10 billion years before our planet formed.

But isn't that kind of just kicking the can down the road?

Would an extra 10 billion years really make it much more likely that life arose and evolved by random, undirected processes?

dlofnep · 09-02-2013 10:40PM

mickrock wrote: »

But isn't that kind of just kicking the can down the road?

Would an extra 10 billion years really make it much more likely that life arose and evolved by random, undirected processes?

Evolution is not random. It is driven by natural selection.

Sarky · 09-02-2013 10:57PM

Mickrock, why haven't you bothered to read a book on these topics? Most of your questions are, not to put too fine a point on it, indicative of a near-total ignorance of evolution and molecular biology.

Please educate yourself.

Popinjay · 09-02-2013 10:57PM

dlofnep wrote: »

Evolution is not random. It is driven by natural selection.

Is there any chance of a keyboard shortcut that will automatically type this sentence?

nagirrac · 09-02-2013 11:09PM

dlofnep wrote: »

Evolution is not random. It is driven by natural selection.

A lot of the confusion regarding evolution hinges on this question. The mechanism for generating genetic variation is commonly believed to be random mutation, whereas how likely an individual is to survive and reproduce is based on how well its traits, defined by its DNA, are suitably adapted to its environment. The genetic mechanism is believed to be random but the outcome is highly predictable.

We are just now learning the details of how DNA actually functions. As these details unfold we may well have to update our thinking on the mechanisms behind evolution. Random genetic mutation is very consistent with DNA that has 98.5% "junk", not so consistent if there is no junk and all of DNA is highly functional biologically. There is no firm evidence yet for the last part of the prior statement but the evidence seems to be heading in that direction.

The Mad Hatter · 10-02-2013 10:48AM

Popinjay wrote: »

Is there any chance of a keyboard shortcut that will automatically type this sentence?

TextExpander?

Sycopat · 10-02-2013 11:14AM

mickrock wrote: »

Lenski's E.coli gained an advantage by the breaking or blunting of existing functional information. Nothing new was created, whether genes or molecular machinery.

It's hardly a ringing endorsement of the supposed creative power of Darwinian mechanisms.

Supposed creative power? Hang on, you do realise that evolution is a slow process of iteration? These E.coli are a good example of evolution because it's a small change that proves useful and so becomes fixed in the population.

At this point of the thread the idea that I should still have to explain to you, who's been in it for so long, such basic tenets of evolution is absolutely ****ing ludicrous.

Your issues with it btw are exactly what makes it a good example.

A cluster of unicellular organisms isn't a muticellular organism.

Isn't it? There's no difference in the genetic data present in any of the different cells in the different tissues of your body after all.

Well, as long as you discount your microbiota ofc.

There are differences between a cluster of unicellular organisms and a multicellular one, but I doubt you know what they are.

More importantly, the slow gradual change predicted by evolution would absolutely require such an intermediary 'multi-unicellular' stage.

"Sceptics, however, point out that many yeast strains naturally form colonies, and that their ancestors were multicellular tens or hundreds of millions of years ago. As a result, they may have retained some evolved mechanisms for cell adhesion and programmed cell death, effectively stacking the deck in favour of Ratcliff's experiment.
"I bet that yeast, having once been multicellular, never lost it completely," says Neil Blackstone, an evolutionary biologist at Northern Illinois University in DeKalb. "I don't think if you took something that had never been multicellular you would get it so quickly.""

http://www.newscientist.com/article/mg21028184.300-lab-yeast-make-evolutionary-leap-to-multicellularity.html

Oh yes, this is a possible explanation, but the retention of some of the features of multicellular life would just mean that unicellular yeast have a shorter road to evolve it again than other organisms. Which would actually explain why it evolved so rather astoundingly rapidly.

Indeed look again at what the skeptical objection actually is.

"I don't think if you took something that had never been multicellular you would get it so quickly."

He's not disagreeing with the principle of unicellular to multicellular occuring. He's pointing out that evolution doesn't usually happen that fast.

I'd also point out that this argument hinges on accepting that the yeast in question are engaged in a multicellular lifestyle...

I refer to it as Darwinism because everyone knows that it is blind and undirected.

Except it's not either of those things. Natural selection is actually the mechanism by which it is neither of those things. Once again you fundamentally fail to understand evolution.

I believe in evolution and that it is an intelligent, directed process. If I referred to Darwinism as evolution we'd be talking at cross purposes.

I don't give a rats that you have a pet belief you want to call evolution. It's not evolution. Evolution is taken. And I see no compelling reason to continue to indulge your silly personal nomenclature at the expense of others who may read the thread. Your belief seems to be Intelligent Design.

The only one who would be talking at cross purposes if everyone else started using the correct terminology would be you.

Sycopat · 10-02-2013 11:53AM

nagirrac wrote: »

The ENCODE project has looked at the functionality of DNA in a variety of human cells. The tentative conclusions are that 80% of DNA is biologically active and involved in regulation within human cells.

Pretty sure the 80% figure only comes about because they included the regions near binding sites which don't actually do anything other than take up space.

It is regulation that turns genes on and off, for example leading to one type of cell becoming a brain cell and another a skin cell. The study has only looked at 147 types of cells so far and as the human body has thousands of different types of cells, there are strong reasons to suggest that the 80% number wll rise to 100% after further research.

No there aren't.

Regulation is what turns genes on and off and we know lots about regulation at a local scale. What's exciting about this type of work is that we'll be able to start looking at regulation as the genome wide process we've always suspected it was. I don't see why that implies that everything is biologically active. I see the number dropping myself. Just like the predicted number of protein coding genes dropped constantly to it's current amounts.

Indeed I could see a debate for not counting every single binding site as 'biologically active' in order to reduce confusion between the physical modification of the chromatin structure to make a gene available/unavailable for transcription, and the transcription of a gene. Although I'd probably land on the against side of said debate.

That said by a loose definition of biologically active, well the entire genome gets reproduced at replication. That's biological activity, no doubt about it. Hmmm maybe we should just put more emphasis on 'biological activity' being a huge umbrella term... Anyway, just typing out loud.

The initial results published by the ENCODE team has been vigerously debated in scientific and non scientific circles. Some of the attacks on the researchers are incredible, given the scope of the project and the fact that the scientists are just reporting their results and not drawing any conclusions as yet. The problem for many scientists and especially non scientists is that the results suggest intelligent design causation rather than random causation so of course they must be wrong. I don't think we have ever seen such an example of anti-science hysteria in action, perhaps since Gallileo's time.

Not in what I've read. Where did you get that idea? Seriously I'd like to read that and you're usually good for a source.

The next 5 years will be fascinating as the ENCODE project proceeds and evolutionary biologists fit the results into evolutionary models. We could well be on the cusp of another major breakthrough in our understanding of how evolution progresses.

This one, yes. Definitely. It's very exciting. Although more so from a genetics rather than evolutionary point of view. We might finally be able to start figuring out how the genome as a whole is regulated and how differentiation works. We've been building up to this with gene level perturbation and expression experiments for some time now so it's really cool to see all this stuff starting to come together.

Zombrex · 10-02-2013 12:23PM

mickrock wrote: »

Could you give some examples of all these new functions? (I hope it's something more than the likes of antibiotic resistance and Lenski's E.coli.)

Are there any observed examples of the "new" species ever being more complex than the one it "evolved" from?

I'm almost certain that this has never been observed.

No, I question Darwinism for not making sense.

If I give the examples to all the things you ask will you promise to stop arguing that Darwinian evolution is unsupported, or at the very least simply go away?

darjeeling · 10-02-2013 01:38PM

Having had a bit more time to respond to the discussion of ENCODE, here's a fuller version of what ENCODE found, and what went wrong in the reporting.

The ENCODE project gives us a new understanding of how the genome functions, and an atlas of all the regulatory features in the DNA sequence that allow it to function. Publication of the results should have been cause for celebration. However, the authors of the main paper spoiled things with an extravagant claim for the amount of functionality in the genome. This claim formed the basis of most of the media reporting.

Here's what the main paper said:

ENCODE wrote:

The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome.
[...]
Operationally, we define a functional element as a discrete genome segment that encodes a defined product (for example, protein or non-coding RNA) or displays a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure). [...]
The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type. (link)

The media turned 80% 'biochemical function' into 80% 'biological function', then (in more exaggerated reporting): 80% of the genome is essential gene switches that control the genes that make us healthy or sick. URL="http://thefinchandpea.com/2012/09/06/encode-media-fail/"]Good summary of media here[/URL.

What 'functionality' did ENCODE find?

- That most of the genome's DNA gets copied into RNA, often at low levels (less than one copy per cell for many sequences).
- Binding sites in the DNA for proteins involved in activating genes
- Sequences that may enhance or repress gene activity, or help decouple activity at one gene from its neighbour.

The regulatory sequences lie outside the 1-2% that ultimately codes for proteins, as do most of the sequences detected as RNA copies.
None of this is unexpected; the principles of gene regulation have been understood for decades. The novelty is in the detail, which is far more extensive than what we've had before.

So what's the problem?

The >80% functional claim, distorted into a claim of over 80% of the genome being necessary for the organism. This goes against some long-established facts of biology. To take two:

1) Genome size varies hugely, and has little bearing on organism complexity.
Puffer fish = 0.4Gb <

> Human, mice = 3Gb <

> Salamanders ~ 35Gb
Does a human or a mouse need almost ten times as much information as a fish? Does a salamander need ten times more still? Why do some amoebas have genomes hundreds of times bigger than ours?
URL="http://www.genomesize.com"]Explore genome sizes at http://www.genomesize.com[/URL

2) Known 'junk' DNA. This hasn't gone away, despite some of the headline claims.

Genomes contain transposable genetic elements, DNA sequences that replicate themselves and insert copies randomly into our genomes in a manner similar to retroviruses. Numbers vary between species: they account for just 2% of the puffer fish genome, and ~80% of some amphibian genomes. The human genome contains literally millions of degraded transposable elements that have jumped all over the place, with a small fraction still active today. In total, they add up tp over 40% of our genome. While most copies are neutral, some are shown to cause disease, and a smaller proportion may be functionally useful to the organism. This, though, is a chance occurrence; the elements are just busy copying themselves, as selfish genes will URL="http://www.sciencedirect.com/science/article/pii/S0378111912008931"]review here[/URL.

We also know of lots of pseudogenes that are no longer functional due to mutation. To take one well studied group, we have over 400 degraded pseudogenes for olfactory receptors (genes for detecting odours) that once were functional link. In all, there are around 15,000 pseudogenes in the human genome, according to the current Ensembl genome assembly.

Given these facts, ENCODE needed to provide good evidence to justify claiming that >80% of the genome is functional. But their definition of 'functional' sets the bar so low as to be meaningless.

What is lacking, as many scientists have commented, is a good basis for comparison. An interesting thought experiment proposed by Sean Eddy is to synthesise a full chromosome of randomly-generated sequence, then to drop it into a cell line and apply ENCODE's battery of analyses. What percentage of this genuine junk would end up being classed as having a 'biochemical function'? Quite a lot, we can expect. A parallel ENCODE project on vertebrates with very large and very small genomes would also be illuminating. Study a salamander, and I'd bet that 80% of its bloated genome would turn out to be 'biochemically functional' too, according to the ENCODE definition.

The ENCODE scientists should have been more careful in their comments to the press, as they managed to give a quite false impression of their findings, and one that has been seized on by creationists and intelligent design advocates as supporting their pseudoscience.

darjeeling · 10-02-2013 01:39PM

nagirrac wrote: »

Random genetic mutation is very consistent with DNA that has 98.5% "junk", not so consistent if there is no junk and all of DNA is highly functional biologically. There is no firm evidence yet for the last part of the prior statement but the evidence seems to be heading in that direction.

There's no requirement in evolutionary theory that there should be junk DNA. Amount of junk varies widely between species, after all. If it were disadvantageous, it would be selected against, and genomes would be very compact. Its existence, though, is a fact. The problem is only for creationists and intelligent design believers, who find junk DNA very inconvenient.

nagirrac · 10-02-2013 07:46PM

darjeeling wrote: »

There's no requirement in evolutionary theory that there should be junk DNA. Amount of junk varies widely between species, after all. If it were disadvantageous, it would be selected against, and genomes would be very compact. Its existence, though, is a fact. The problem is only for creationists and intelligent design believers, who find junk DNA very inconvenient.

I agree that creationists and some believers in intelligent design are dishonest in how they try and interpret and spin scientific findings. However, they are not the only ones who do this.

Richard Dawkins from The Greatest Show on Earth (2009, 3 years ago), in the context of how junk DNA is useful for mocking creationists and those who believe in intelligent design: " it is a remarkable fact that the greater part (95% in the case of humans) of the genome may as well not be there, for all the difference it makes". In other words such a high percentage of junk DNA is what you would expect from the messy process of random mutation over millions of generations.

Since the preliminary results of the ENCODE project, Dawkins has changed his tune and in recent debates has said that what was thought to be junk DNA now being found to be vital for life's function was "exactly what a Darwinist would expect". If that isn't moving the goalposts I'm not sure what is.

nagirrac · 10-02-2013 08:31PM

Sycopat wrote: »

Not in what I've read. Where did you get that idea? Seriously I'd like to read that and you're usually good for a source.

Thanks for the great response.

My background is not biology, it is chemistry so I tend to look at things from a chemical evolution standpoint. I formed my opinion of likely intelligence behind the universe based on a number of fields that I am interested in; cosmology, quantum physics, chemistry, biology, evolutionary biology, the brain, the mind, consciousness, and information theory. Thats a lot to cover but I try and keep up as best I can and try and look at life through many lenses.

I think it is fair to say that the majority of scientists are completely immersed in their field of study. There are very few who ask "why" questions, even in their own field, as their work involves trying to find the "how" things work and not why.

What is most fascinating to me is that in all areas of science as we uncover more and more evidence, have information at their core. I understand that word brings up "creationist" mental images, but the only thing we can reasonably align information with is intelligence. The question really is are all these sources of information related, quantum mechanics, the RNA/DNA coding that defines life, information processing among neurons in the brain, the emergence of consciousness, and in recent decades the human expansion of digital information. The study of consciousness is the most interesting to me and where I believe we will ultimately find more answers.

Although I am not in any sense an expert in evolutionary biology I don't believe there is currently any answer for how such an information rich, digital code like DNA evolved. I lean towards an integrated information flow process in the universe that leads to life as we know it, my source for that is what I have read from the work of Christof Koch and Giulio Tononi, both of whom have written fascinating books on consciousness. Like these authors I tend to believe that consciousness is a fundamental property of the universe and not merely an emergent property of the brain.

Delirium · 10-02-2013 08:39PM

Does the idea of ID not just push the origin of life question back to be answered later? If as you say a designer created life, who created the designer? And how is that to be answered without invoking a deity at some point?

nagirrac · 10-02-2013 08:58PM

koth wrote: »

Does the idea of ID not just push the origin of life question back to be answered later? If as you say a designer created life, who created the designer? And how is that to be answered without invoking a deity at some point?

These are questions that we ask from the framework of our observed universe, and the primary question is related to time. Time is a difficult concept invoking many paradoxes, what came before the big bang? what does infinity or eternal mean? etc.

If our universe is a subset of a larger universe where the parameters are different, all bets are off. In such a greater universe there may be no time as we know it, maybe it just is. In some ways this is a logical answer to the paradoxes involving time.

The only subjective evidence we have for such a larger universe are those reported by "out of body" experiences, especially those who can get into this mental state deliberately. Impossible to verify but interesting nontheless.

Zombrex · 10-02-2013 09:18PM

nagirrac wrote: »

I agree that creationists and some believers in intelligent design are dishonest in how they try and interpret and spin scientific findings. However, they are not the only ones who do this.

Richard Dawkins from The Greatest Show on Earth (2009, 3 years ago), in the context of how junk DNA is useful for mocking creationists and those who believe in intelligent design: " it is a remarkable fact that the greater part (95% in the case of humans) of the genome may as well not be there, for all the difference it makes". In other words such a high percentage of junk DNA is what you would expect from the messy process of random mutation over millions of generations.

Since the preliminary results of the ENCODE project, Dawkins has changed his tune and in recent debates has said that what was thought to be junk DNA now being found to be vital for life's function was "exactly what a Darwinist would expect". If that isn't moving the goalposts I'm not sure what is.

There are two different goals.

Junk DNA was not used to support Darwinism, it was used by Dawkins as an attack on Creationist ideas that the DNA of life was intelligently created.

That seems ridiculous for a number of reasons, one of which was junk DNA. And since the Encode project found that 80% of DNA does something, that still leaves 20% not doing anything. Of course Creationists will just say that the encode project demonstrates we should not assume it does nothing.

The comment he made about a Darwinian expecting this is a different matter, it is what a Darwinian would expect. The junk DNA was not in support of Darwinism, in fact Darwinism had trouble with it too. It is reassuring for Darwinism that much more of the DNA does something that we previously thought, because the idea of so much waste seemed some what odd in a Darwinism context. You still expect junk DNA of some level with Darwinism, and you still find it with the Encode Project.

Don't make the mistake of assuming that changing an attack on Creationism is altering support for Darwinism and vice versa. There are lots of reasons to be critical of Creationism that don't relate to support for Darwinism.

endacl · 10-02-2013 09:25PM

Whatever people think of Dawkins, they'd have to take note of the fact that he changed his position in response to new understanding of new information. Mickrock take note. Provide new information, or a new understanding of old, and you'll see tunes change. Give the hamster a day off.

darjeeling · 10-02-2013 09:31PM

nagirrac wrote: »

I agree that creationists and some believers in intelligent design are dishonest in how they try and interpret and spin scientific findings. However, they are not the only ones who do this.

Indeed, the whole ENCODE controversy was about spin, though I think it was done to play up the importance of the work in the public estimation, and not to mislead.

nagirrac wrote: »

Richard Dawkins from The Greatest Show on Earth (2009, 3 years ago), in the context of how junk DNA is useful for mocking creationists and those who believe in intelligent design: " it is a remarkable fact that the greater part (95% in the case of humans) of the genome may as well not be there, for all the difference it makes". In other words such a high percentage of junk DNA is what you would expect from the messy process of random mutation over millions of generations.

Since the preliminary results of the ENCODE project, Dawkins has changed his tune and in recent debates has said that what was thought to be junk DNA now being found to be vital for life's function was "exactly what a Darwinist would expect". If that isn't moving the goalposts I'm not sure what is.

I think it is still the case that most of the human genome is non-essential for producing a fully functional human being. Just how little is required is not clear - perhaps between 10 and 20%, going on all the circumstantial evidence from genomics. ENCODE, for all its achievements, hasn't given any reason to think the figure should be much higher. However, it's not possible to put this to the ultimate test and see if an embryo with a genome filleted of 'junk' would develop normally.

As for what Dawkins has said, I've not seen his quotes myself so I can only go on what you've posted. I don't see that your paraphrasing ('In other words such a high percentage of junk DNA is what you would expect ...') is a logical extension of the quote you cite. I don't know specifically what he thought was 'exactly what a Darwinist would expect' so I can't comment on that, or on whether or not he has changed his views.

What I have seen from creationists / ID supporters is attempts to deny that there is such a phenomenon as junk DNA, because they seem to consider it irreconcilable with a carefully designed genome. If this is the creationist/ID position, then pointing out the existence of junk DNA is a legitimate critique.

nagirrac · 10-02-2013 10:20PM

Zombrex wrote: »

That seems ridiculous for a number of reasons, one of which was junk DNA. And since the Encode project found that 80% of DNA does something, that still leaves 20% not doing anything. Of course Creationists will just say that the encode project demonstrates we should not assume it does nothing.

What is ridiculous is to rule in or rule out intelligence behind the emergence of the universe or the emergence of life or the development of a mind that can ask these questions when we do not know.

The ENCODE project, so far, has looked at 147 different types of human cells which is a subset of the total number of types of human cells (over 200 I believe?). I don't know enough about epigenomics to tell what one would expect when the full range of cells are studied, but it would seem logical that further functionality would be found.

Epigenomics is a pretty recent field of study so we should expect a lot more information to come out in the years ahead. It is now clear that DNA codes two different types of information, one (genomics, how our ~20,000 proteins are made) we know relatively a lot about, the other (epigenomics, what genes get activated or turned off in specific cells) we are just starting to understand.

There may even be more layers of information in DNA we are not aware of yet, just as we were not aware of DNA's structure up to 60 years ago, not aware of the exact number of genes and their function up to a decade ago and just now learning about specific cell regulation.

Sarky · 10-02-2013 10:54PM

As someone who works in and about that field nagirrac, I sincerely doubt it'll turn out like to seem to want it to.

nagirrac · 11-02-2013 01:09AM

Sarky wrote: »

As someone who works in and about that field nagirrac, I sincerely doubt it'll turn out like to seem to want it to.

What I might want or anyone else might want though is irrelevant Sarky. It is the way it is and assuming our brains/minds continue to evolve at the rate they have been evolving we will continue to figure it out. That's the important part, speculation is for fun.

Lucy8080 · 11-02-2013 04:09AM

Nagirrac asked .." What does infinity or eternal mean?"

I'd like to hear that question answered from the position of both creationist / evolutionary scientists.

Or any scientists, or anybody.

Might be worth looking at!

And what we think we mean when we use these words.

Zombrex · 11-02-2013 11:56AM

nagirrac wrote: »

What is ridiculous is to rule in or rule out intelligence behind the emergence of the universe or the emergence of life or the development of a mind that can ask these questions when we do not know.

Why is that ridiculous other than some people like the idea of an intelligent creator?

We have natural processes that account for life, why introduce an intelligence. Its like saying that it isn't gravity pulling you down, it is tiny invisible fairies pushing you don't. Would it be ridiculous to rule that out?

nagirrac wrote: »

There may even be more layers of information in DNA we are not aware of yet, just as we were not aware of DNA's structure up to 60 years ago, not aware of the exact number of genes and their function up to a decade ago and just now learning about specific cell regulation.

True, but again this doesn't increase support for intelligent design. Quite the opposite in fact.

The only controversial thing here is that Dawkins had an argument against intelligent design that turned out to be not much of an argument. Luckily there are a million other arguments against intelligent design, so I wouldn't stress over it.

Genghiz Cohen · 11-02-2013 11:59AM

Lucy8080 wrote: »

Nagirrac asked .." What does infinity or eternal mean?"

I'd like to hear that question answered from the position of both creationist / evolutionary scientists.

Or any scientists, or anybody.

Might be worth looking at!

And what we think we mean when we use these words.

NUMBERPHILE!

https://www.youtube.com/watch?v=elvOZm0d4H0

doctoremma · 11-02-2013 02:25PM

nagirrac wrote: »

What is most fascinating to me is that in all areas of science as we uncover more and more evidence, have information at their core.

I am intrigued by this statement and would like to add some ponderings (I am, in no way, "qualified" to debate this specific point)....

Would it not be fair to say that "information" is a construct of the human experience? Does nature, either biologically/chemically/physically, hold "information"?

For example, when we think about a gene that provides a template for mRNA production, which in itself provides a template for polypeptide production, we talk about the characteristic of "information" being read and transmitted. However, not the gene nor the mRNA nor the protein has any need for this characteristic of "information". It just happens, chemistry and all that.

I don't see that the gene contains any more "information" than the free radical seeking its next monomer target in a polymerisation event, nor that contained in the filled spaces of a beehive lattice.

So, to come back to your statement, I don't find it the least bit surprising that we seem to be uncovering more and more "information" at the core of natural processes. That's because "information" is something we apply to what we observe. And the only intelligence required is in ourselves.

doctoremma · 11-02-2013 02:39PM

mickrock wrote: »

Could you give some examples of all these new functions? (I hope it's something more than the likes of antibiotic resistance and Lenski's E.coli.)

But...but...even these things, which you appear to be regard as piffling, are (to me, at least) amazing events. That they don't impress you suggests that you have an entirely warped outlook on biology - and standards set far too high to be compatible with evolution.

Or perhaps your idea of "miraculous" has been distorted by some of the stories you've been reading?

You want the new and amazing ability that, I don't know, allows us to sense magnetic fields or shoot lasers from our eyes? X-Men and all that? Do you have any idea of the massive number of genes and processes required to even grow a fingernail, let alone a brand new organ that allows us to sh*t gold. It can't and it won't happen - evolution does not leap and bound to produce a kidney in any observable timescale (at least, since we've been measuring).

mickrock wrote: »

Are there any observed examples of the "new" species ever being more complex than the one it "evolved" from?

Define "complexity". *sigh*

"The Origin of Specious Nonsense"

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