"The Origin of Specious Nonsense"

26-01-2013 03:30PM

mickrock wrote: »

About 4.5 billion years old.

OK so do you see the difference between a thousand years of selective breeding and all those millions upon millions of years of evolution? Do you understand just how intense competition within (and without :P ) species actually is?

kiffer · 26-01-2013 03:31PM

mickrock wrote:

Similarly in the wild there are limits to how far an organism can change by Darwinian means.

kiffer wrote: »

What.
Are.
Those.
Limits?
[Citation needed]

... seriuosly, so what you are saying is that yo have no idea what those limits are.

mickrock wrote: »

By this stage the limit has been pretty much reached on how much more dogs can change by selective breeding.

Millions of years can make massive changes but the Darwinian mechanisms of random variation and natural selection don't seem to be capable of the job.

Don't seem to be capable of it according to whom?
A millon tiny changes add up.
1+1+1+ ... (thousand of operations ) ... +1=big number.

darjeeling · 26-01-2013 03:36PM

An oft-repeated claim is that new genetic information cannot be produced through variation and natural selection, and cannot account for the evolution of complex organs, biological systems etc. The genome revolution is now showing us what is actually happening.

Within humans, we find all sorts of mutations - whole chromosomal duplications and fusions, partial duplications, deletions, translocations and inversions, point mutations, polynucleotide expansions and deletions. All are potential targets for natural selection.

Until very recently, we didn't appreciate how much variation there was in normal, healthy people, as most focus was on pathological mutations. Now, with projects such as the thousand genome project, we're seeing the real extent of variation. One striking finding has been the discovery of copy number variation (CNV) of regions of kilo- to mega-bases, meaning that two people can have different numbers of copies of a given gene due to local duplication of sections of chromosome.

When comparing genomes between different animal species, we see the same types of variation that we find within humans. Comparing species whose divergence can be dated using fossil evidence, shows that the more distantly related species have more accumulated mutational changes between them. However, there is no qualitative difference seen between comparisons of closely and distantly-related animal species.

Comparing animal genomes typically shows a high to very high level of conservation of genes, though we do see gene gain and loss. Gains are mostly through tandem duplication of existing genes, followed by DNA sequence divergence between the duplicates. Sometimes an ancestral duplicate is lost in one or more daughter species, and sometimes genes are lost altogether when they have ceased to be useful.

Much rarer is de novo formation of genes from sequences that weren't previously genes. The 2011 PLoS One paper mentioned earlier reported around 60 such events in humans. However, the paper also shows these new 'genes' barely meet the usual criteria for a gene - the genes are short, simply-structured sequences with no evidence for function, transcription above the background level of the genome as a whole or any control of expression. One of the features lacking helps illustrate how we know that natural selection is acting at functional genes: the novel 'genes' do not show the same reduced mutation level that we see at most normal genes, which is due to natural selection removing deleterious mutations in these functional genes.

What all this shows us is that the differences between, say, placental mammals tend not to be due to the appearance of complex, completely novel genes arising out of nowhere, but through modifications of existing genes. And perhaps the most significant differences are not due to changes within the protein coding sequences of the genes themselves, but to changes in the way that genes are regulated.

Until the last few years, we didn't know that much about gene regulation. Ongoing work is revealing how small regulatory sequences and methylation sites in the vicinity of genes can, through interaction with proteins, affect the amount of gene product made and the circumstances in which it is made. Variations at these sites can be seen to alter the amounts of proteins made, with consequences for the biology of the cell and the organism. The regulatory sequences are far simpler than the genes, and are seen to be much more rapidly evolving when we compare the genomes of different species, hence the emerging picture is that differences between, say, mammals owe much to changes in the way that a core set of genes is regulated: different ways of playing the same hand.

Things are, of course, very different when you look at the other end of the biological spectrum - at the bacteria that Sarky is working on. Bacteria are more numerous by many orders of magnitude than us, have life cycles that are shorter by many orders of magnitude, are less fastidious in replicating their DNA and are more likely to swap DNA with quite distantly related bacteria in a way that plays havoc with attempts to create a branching evolutionary tree. This way of life, whcih prevailed through most of our evolutionary ancestry, is much more likely to produce novel, functional genes from time to time. Our understanding is increasingly that the most of the building blocks for animals originated way back in time.

I hadn't quite meant for this to turn into an essay. Oh well...

swampgas · 26-01-2013 03:54PM

mickrock wrote: »

<snip>
I don't think it's logical that a series of many small steps resulting from a blind, undirected process could produce the complexity we see in life forms.

Actually, I think this is an interesting point. Intuitively, it's hard to see how simple steps and simple rules can produce great complexity. So, intuitively, we may feel that random mutations should not increase complexity at all.

However, this is another case where our intuition is faulty. Chaos theory, fractals, and emergent bahaviour started to be much better understood in the 1980s and explain how complexity can emerge from very simple systems.

See:

http://en.wikipedia.org/wiki/Chaos_theory
http://en.wikipedia.org/wiki/Emergence

And if you want to see how stunningly beautiful patterns can emerge from very simple rules, check out the Madelbrot set:

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

endacl · 26-01-2013 04:27PM

mickrock wrote: »

By this stage the limit has been pretty much reached on how much more dogs can change by selective breeding.

Millions of years can make massive changes but the Darwinian mechanisms of random variation and natural selection don't seem to be capable of the job.

They've seemed very capable thus far. Are you trying to fix the bingo game...?

endacl · 26-01-2013 04:36PM

mickrock wrote: »

The point I was making with selective breeding is that when an animal is bred for a certain trait a limit will be reached in a relatively short time. An animal bred for its size will not continually get bigger and bigger. There is a limit to how much it will grow.

Similarly in the wild there are limits to how far an organism can change by Darwinian means.

Who says a limit has been reached? That's like arguing that the M1 doesn't go from Dublin to Belfast, just because at some arbitrary point you're not there yet. And compounding the stupidity by refusing to accept you started in Dublin at all. Even though you have a receipt from a filling station in Swords.

I kinda hope, in a strange way, that you don't at some point figure this stuff out for yourself. I can only imagine what the realisation of such monumental stupidity would do to self confidence of such epic blowhardinian proportions...

mickrock · 26-01-2013 05:47PM

darjeeling wrote: »

An oft-repeated claim is that new genetic information cannot be produced through variation and natural selection, and cannot account for the evolution of complex organs, biological systems etc. The genome revolution is now showing us what is actually happening.

Within humans, we find all sorts of mutations - whole chromosomal duplications and fusions, partial duplications, deletions, translocations and inversions, point mutations, polynucleotide expansions and deletions. All are potential targets for natural selection.

I notice that when you mention mutations you don't say random mutations. It seems likely that non-random mutations play a more important role in evolution than random ones:

A Biochemical Mechanism for Nonrandom Mutations and Evolution:

"As this minireview is concerned with the importance of the environment in directing evolution, it is appropriate to remember that Lamarck was the first to clearly articulate a consistent theory of gradual evolution from the simplest of species to the most complex, culminating in the origin of mankind (71). He published his remarkable and courageous theory in 1809, the year of Darwin's birth. Unfortunately, Lamarck's major contributions have been overshadowed by his views on the inheritance of acquired characters. In fact, Darwin shared some of these same views, and even Weismann (106), the father of neo-Darwinism, decided late in his career that directed variation must be invoked to understand some phenomena, as random variation and selection alone are not a sufficient explanation (71). This minireview will describe mechanisms of mutation that are not random and can accelerate the process of evolution in specific directions. The existence of such mechanisms has been predicted by mathematicians (6) who argue that, if every mutation were really random and had to be tested against the environment for selection or rejection, there would not have been enough time to evolve the extremely complex biochemical networks and regulatory mechanisms found in organisms today. Dobzhansky (21) expressed similar views by stating “The most serious objection to the modern theory of evolution is that since mutations occur by ‘chance’ and are undirected, it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye.”

http://jb.asm.org/content/182/11/2993.full

doctoremma · 26-01-2013 05:55PM

mickrock wrote: »

it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye.

I AM going to read the article but I just need to say here: the human eye is NOT beautifully designed. The retina is entirely counterintuitive for a start. Almost like nature works with what its given.

Ziphius · 26-01-2013 06:04PM

It's an interesting article mickrock but it seems to hinge on the semantics of the word random. If mutation was truly random it would affect each locus with equal likelihood. Evidence, however, suggests that genes mutate at different rates. Perhaps due to the secondary structure the DNA molecule happens to form or because a larger gene presents are greater "surface area" for a mutagen or for numerous other reasons.

It doesn't take away from the fact that mutation causes variation which is then selected by the environment -- evolution. I'm not sure how this supports your point.

darjeeling · 26-01-2013 06:10PM

mickrock wrote: »

I notice that when you mention mutations you don't say random mutations. It seems likely that non-random mutations play a more important role in evolution than random ones:

A Biochemical Mechanism for Nonrandom Mutations and Evolution:

http://jb.asm.org/content/182/11/2993.full

The paper you cite describes the possibility of directed evolution in bacteria. If you read down, you will find that it specifically points out that the proposed mechanism will not apply in higher animals, in which the cells that form the next generation are isolated very early in embryogenesis from the rest of the animal, and so are not affected by mutations elsewhere in the animal.

That said, there is evidence for variability in mutation rates throughout the genome of humans and other animals. Some of this variability may itself have been selected through evolution, perhaps as a way of generating novel versions of proteins that play a role in arms races between host and pathogen, for example. Still, the individual mutations that occur remain essentially random so far as we can tell.

doctoremma · 26-01-2013 06:12PM

OK, read it. For those who don't want to bother (and are willing to accept my summary):
1. Mutations can happen when the DNA undergoes various chemical changes/environmental insult etc.
2. DNA in certain states is likely to be more exposed to 1.
3. DNA undergoing transcription falls into category 2.
4. Transcriptionally-active DNA is therefore more likely to undergo mutations.
5. Therefore, the type of mutation that can drive evolution most effectively e.g. by altering a metabolic pathway, is likely to be a "non-random" mutation in functionally important pathway.

I'd be interested to see if Sarky has anything to comment here, given the bacterial biochem content.

However, Mickrock, I'm not sure it supports the premise you think it supports. I'm not sure when any of us talk about "random" mutations, we are excluding anything in that paper. We use "random" to differentiate from "directed" (either by the hand of a creator, or by a mechanism that has a goal in mind).

And the references to Lemarckism in the introduction are a non-sequiteur (IMO).

Barr125 · 26-01-2013 06:30PM

mickrock wrote: »

I notice that when you mention mutations you don't say random mutations. It seems likely that non-random mutations play a more important role in evolution than random ones

The evidence behind the idea of "non-random" mutations is still in the early stages, as the mechanisms behind it haven't yet been described. But all "non-random mutations" seem to be, from my own reading, are the optimizing of the evolutionary process to reduce the development of deleterious mutations.

OK, 2 remarks. 1 is that the non-random mutations still look random to me. All that has happened is that the hindering mutations have been reduced and will now cycle through the neutral and adventitious mutations for the best one. This looks like the Winning Streak of nature. You're guaranteeing a win , but it's all about how much.
The 2nd is that what mutations are adventitious, neutral or deleterious is completely down to the organisms environment. Example, a snake develops the ability to breath underwater, one that doesn't hinder its regular breathing system. You would think that with all the rivers, lakes and the fact that the Earth is 70% water, that would be an adventitious mutation. But it means squat when that snakes lives in the middle of the Gobi desert or the Sahara or Death Valley. That mutation has now become neutral, despite it being a really good addition.

The phrase "location, location, location comes to mind. :pac:

mickrock wrote: »

it is difficult to see how mutation and selection can add up to the formation of such beautifully balanced organs as, for example, the human eye.”

If the eye is so beautifully balanced then why are there bats, known as microbats, that have forgone the use of their eyes, despite having them, and opted for echolocation and then a group of Megabats that still use their eyes and do not use echolocation?

kiffer · 26-01-2013 07:11PM

The eye... the human eye no less...
I mean... octopus eyes maybe but human eyes have the whole retina problem, the high rate of colour blindness in men, the poor night vision.
I mean if I was designing human eyes we'd be tetrachromatic and have night vision like cats, have a third eyelid and the ablity to focus while underwater. The blood suply would be on the back of the retina like in octopodes and squid and the nerves wouldn't be hooked up in such a way as to give us a blind spot over a sizeable proportion of our field of vision.

Still, citing the eye moves us one step close to bingo so carry on.

dlofnep · 26-01-2013 07:12PM

Here's an idea - Why don't you come on Skype Mickrock and debate the issue in realtime? We'll quickly see how well your arguments hold up. We could setup a group conversation, and you could invite any of your Creationists on to back you up.

Pushtrak · 27-01-2013 06:29PM

dlofnep wrote: »

Here's an idea - Why don't you come on Skype Mickrock and debate the issue in realtime? We'll quickly see how well your arguments hold up. We could setup a group conversation, and you could invite any of your Creationists on to back you up.

Do one better. Make it a google hangout. That way, you could upload it on youtube and people could see it later.

Edit: I also love how many comments a thread I started got. I think this is my 2nd post in this thread. (Third, actually including OP.)

Zombrex · 27-01-2013 11:40PM

mickrock wrote: »

Why do lots of you want to discuss alternative mechanisms to Darwinism?

If Darwinism is so robust you should easily be able to defend it.

It is easy to defend it, you have been given mountains of evidence. You are simply choosing to ignore it. Which naturally leads everyone else to think why are you really here, what is your true motivation, because generally when someone says "There is no evidence" and is then shown evidence but ignores it, people conclude the person is not genuine.

This is supported by the fact that you claim you accept evolution happens but not by Darwinian means but then say you accept it happens by natural selection but claim that natural selection cannot account for macroevolution (as Creationists would call it)

Well guess what, you just contradicted yourself. Darwinian evolution does not suppose a time scale. The natural selection working on small changes is as Darwinian as anything else.

So when you said you don't accept Darwinian evolution but then proceeded to explain that you do accept essentially Darwinian evolution, all you did was demonstrate you don't understand what these terms mean.

I suspect you are simply repeating jargon you have heard on Creationist websites, without any actual understanding.

So we are left with the following conclusions, you don't understand the subject you are discussing and (perhaps more importantly) don't have any genuine interest in understanding the subject you are discussing.

Which again just calls everyone to question as to why you are actually here.

Trolling would be my guess.

Sarky · 28-01-2013 05:14PM

doctoremma wrote: »

I'd be interested to see if Sarky has anything to comment here, given the bacterial biochem content.

Gimme a few days, I spent the weekend drinking and shouting at things while rolling bucketloads of dice and could do without having to think for a wee while.

Bannasidhe · 28-01-2013 05:16PM

Sarky wrote: »

Gimme a few days, I spent the weekend drinking and shouting at things while rolling bucketloads of dice and could do without having to think for a wee while.

Quickly - now is the perfect time to read some Creationist 'proof'- it will maybe make 'sense'...

:pac:

Sarky · 28-01-2013 09:44PM

Bannasidhe wrote: »

Quickly - now is the perfect time to read some Creationist 'proof'- it will maybe make 'sense'...

:pac:

Ah now, I just don't want to think for a while, not actively become dumber.

mickrock · 03-02-2013 06:49PM

expectationlost wrote: »

life wasn't just acccidently but inevitable. :cool:

I suppose it's inevitable that it happend by chance only if you don't think about it too deeply.

Obliq · 03-02-2013 06:57PM

mickrock wrote: »

I suppose it's inevitable that it happend by chance only if you don't think about it too deeply.

Oh noes.

Well, I just enjoy the wonder of chance - there is quite enough deep meaning in being a little mote of life in this unimaginably vast universe without trying to make this little mote of life specially put here by a sky fairy.

I hope you're going to watch the program?

expectationlost · 04-02-2013 12:44PM

mickrock wrote: »

I suppose it's inevitable that it happend by chance only if you don't think about it too deeply.

i think he strongly made his point in the first ep

http://twitter.com/profbriancox/status/296595461207375872
Listened to "Thought for the Day". Science's explanation for life's complexity is NOT that it emerged by chance. Precisely the opposite!

mickrock · 04-02-2013 10:26PM

expectationlost wrote: »

i think he strongly made his point in the first ep

http://twitter.com/profbriancox/status/296595461207375872
Listened to "Thought for the Day". Science's explanation for life's complexity is NOT that it emerged by chance. Precisely the opposite!

Atheists who believe that the origin of life didn't happen by chance.

Whatever next?

The Mad Hatter · 04-02-2013 10:58PM

mickrock wrote: »

Atheists who believe that the origin of life didn't happen by chance.

Whatever next?

Who let you out of the sack?

Sarky · 05-02-2013 02:47AM

mickrock wrote: »

Atheists who believe that the origin of life didn't happen by chance.

Whatever next?

Oh just stop it, you're embarrassing yourself. And read a book or two on evolution like we keep asking. You'll never understand it if you keep running away from it like a big girl's blouse.

mickrock · 05-02-2013 04:11AM

Sarky wrote: »

Oh just stop it, you're embarrassing yourself. And read a book or two on evolution like we keep asking. You'll never understand it if you keep running away from it like a big girl's blouse.

You're getting confused again.

I was talking about the origin of life, not evolution. These are considered separate matters by people who talk about evolution. A bit of a schoolboy error there.

magicbastarder · 05-02-2013 10:24AM

Cork boy 55 wrote: »

I find his manner of communication annoying and his personnel dress sloppy
Why he is not wearing a tie. An Oldham accent WTF

WTF indeed.

Doctor Strange · 05-02-2013 11:47AM

mickrock wrote: »

You're getting confused again.

I was talking about the origin of life, not evolution. These are considered separate matters by people who talk about evolution. A bit of a schoolboy error there.

Then why in the name of sweet Zod have you spent the last month or two talking about increasing complexity?

Start a topic on abiogenesis if that's your concern.

kiffer · 05-02-2013 11:58AM

Mickrock is back?
Hot diggity dang!

kiffer wrote: »

mickrock wrote:

Similarly in the wild there are limits to how far an organism can change by Darwinian means.

kiffer wrote:

What.
Are.
Those.
Limits?[Citation needed]...

seriuosly, so what you are saying is that yo have no idea what those limits are.

mickrock wrote:

By this stage the limit has been pretty much reached on how much more dogs can change by selective breeding.Millions of years can make massive changes but the Darwinian mechanisms of random variation and natural selection don't seem to be capable of the job.

Don't seem to be capable of it according to whom?
A millon tiny changes add up.
1+1+1+ ... (thousand of operations ) ... +1=big number.

So...
What are those limits... roughly... I mean I don't expect much here just back up your comments a little.

Zombrex · 05-02-2013 04:49PM

mickrock wrote: »

I suppose it's inevitable that it happend by chance only if you don't think about it too deeply.

It didn't happen by chance, it happened based on fundamental laws of chemistry. Given these laws, and the size of the universe, life in some form is pretty much inevitable.

But thanks for demonstrate yet another topic you clearly don't know anything about.

"The Origin of Specious Nonsense"

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