Wednesday, September 19, 2007

On increasing information in the genome

Here's something about which I'm fairly curious. I am very skeptical (no, really?) but really would like to know if anyone reading this can furnish an example of a mutation that:
  1. has been observed in an organism NOT IN A LAB (b/c that would inject intelligence into the equation, and I'm after full nature here),
  2. has increased the USEFUL information in the genome,
  3. has been BENEFICIAL for survival in the organism's natural habitat,
  4. which occurred without ANY human intervention whatsoever,
  5. and which has been observed repeatedly.

That's just science. I want to see if evolution fits the bill.
Just to forestall answers I've gotten in the past, I don't want to hear about your bacteria who grew resistant to antibiotics developed by humans, introduced by humans in a petri dish in a lab and who, upon reintroduction into a petri dish full of the original kind of bacteria, died en masse (though no one ever mentions that part). I don't want to hear about peppered moths or finch beaks. The item in question must fit all 5 criteria.

45 comments:

John Morales said...

http://www.talkorigins.org/origins/faqs.html

rotsaP loeJ said...

more relevant and better tasting...
http://www.cheddarsomerset.co.uk/History/Cheddar%20History.htm

rotsaP loeJ said...

aww, it didn't fit www.cheddarsomerset.co.uk/
History/Cheddar%20History.htm

(no space between uk/ and History)

Rhology said...

John,

Is there one (or more) article(s) in particular that deals with it?
If so, do they fulfill the 5 criteria I set out? If not, my interest will flag b/c I'm looking for the overwhelming evidence I keep getting promised exists.

rotsaP loeJ,

Mmmm, cheddar.

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Rhology said...

All hail the overwhelming rationality of the RRS.

chooseDoubt said...

Hi Rhology,

What do you mean by "increasing information"? I'm presuming you mean simply an increase in the amount of base pairs.

If that's the case then please go here (http://www.ncbi.nlm.nih.gov/sites/entrez) and search for "gene duplication". You'll get back over 5000 published papers studying the duplication of genes that already exist within a genome. This is one method by which the number of base pairs is increased. Strictly speaking any new mutation increases the information since it is a new sequence not contained within the previous sequence.

Additionally, such duplicates are individually susceptible to mutation (just as any of the genetic information is) and some of these mutations are "useful", as you put it - the pancreatic enzyme RNASE1 duplication and mutation to RNASE1B in Langur Monkeys, which works better in their more acidic small intestine is one example (Lang et al. 2000). You could also reference the Great EggFly (published July 13 2007 edition of Science) and many hundreds of mutations and genetic exchanges in bacteria that have resulted in drug resistance and other traits, viruses that cross species barriers (influenza, HIV, and many others), all of which have occurred outside the laboratory and all of which have changed, sometimes increasing, the information in the genome.

Another worthwile instance is sexual reproduction. There are numerous genetic diseases that occur because we rely on two of the same gene carried on different chromosomes (muscular dystrophy for example). We are fine with one good and one bad, but when we get two bad then we're in trouble. How precisely would this happen without duplication and mutation? Two different versions means an increase in information over two copies of the exact same gene.

I must point out that your criteria are a bit sloppy, since you at first request only examples that have not been observed in a lab when there currently exist no field equipment to read a genome. The criteria of "useful" is also meaningless. The replicators are the genes and not the individuals or the groups and the simple fact of a genes existence may be considered "useful" to the gene itself.

As for beneficial for the organism, see any of the examples above or spend some time going through the 5396 examples I've linked you to.

All the best,

CD.

PS. I'm back from holidays and will get round to my long over due responses.

chooseDoubt said...

Oooops - sorry. I meant to pick you up on the "observed repeatedly" criteria as well as I think this highlights one of your gravest misunderstandings of evolutionary theory and genetics.

The probability of any particular mutation occurring are billions to one. The exact same mutation occurring independently and repeatedly is obviously less probable. No one expects to see the same mutation occurring repeatedly. What we expect is that mutations that result in an increased probability of that particular gene increasing in frequency within the gene pool will over time increase in frequency within the gene pool by inheritance. This is exactly what we do see, even in the moths and the bird's beaks that you choose to arbitrarily ignore for no good or even stated reason.

rotsaP loeJ said...

I don't know exactly, but I anticipate that in case of the moths R. would say that they represent mere natural selection (light and dark coloured pepper moths already existed in the population and were not, therefore, the result of any new genes as far as can be observed).

Secondly, doesn't 'useful' in the context of evolution entail some survival advantage? That's what we generally mean when we talk about large-scale adaptations; why would the criteria be any different on a genetic level? Obviously there are some mutations we could imagine that are not particularly useful to the gene in question, in the sense that it would subsequently die...

chooseDoubt said...

Hi rotsap loej,

Regarding the moths, whether or not the genes were already in the population rather depends on when one samples the population. There is also no requirement in the theory of evolution by natural selection that a mutation must occur simultaneously or after the selective pressure that selects for it emerges. Some mutations make no or little difference to an organism’s probability of reproduction until a change in environment (including other genes) then creates a selective pressure. For example a gene that gives specific antibiotic resistance is irrelevant until the emergence of that specific antibiotic. A gene that allows a plant to survive a less humid climate than its cousins may make no difference until the climate becomes less humid. A gene that controls the rate of tree growth may make no difference until a new variant emerges that causes faster growth, and so on.

Mutations do not occur due to selective pressure. They occur randomly and independently and may then be subject to non-random selective pressure. One would expect, in the case of severe selective pressures, that the mutation that enables continued replication will already be present in the gene pool due to earlier mutation as if this were not the case then the species concerned would become extinct before further mutation could occur. For less severe selective pressures then mutation may occur before or after the selective pressure begins to exert its force.

As for your defence of the “useful” criteria, that’s an over-simplification and there seems to be little value trying to argue the finer points based on over-simplifications. First off, a great deal of our DNA is junk and has no use to us outside the scope of academic study. The fact that such genes are reproduced in successive generations and the observed truth that there are common and varied versions of specific junk DNA across different populations shows that whilst such genes may be “useful” to themselves (they continue to exist) that the criteria of “useful” does not seamlessly cross the gene-organism boundary.

Cheers,

CD

John Morales said...

Rhology, I dare you to state, (remember: in the sight of God, according to your self-professed belief), that you have perused talk.origins with honest intent to learn about the real claims of evolutionary theory.

Or, you can prove my intuition correct that you did not do so. Because you’re scared of the truth.

Rhology said...

Ah, John, I have ventured but few times into the hallowed realms of talk.origins. Read a few things here and there.

And yes, clearly I am scared of the truth. And if the atheistic worldview is true, then there is no way to ground the communication of that truth or the logic by which it was found. Speaking of which, that is pretty scary...

I'd like to know where I said or implied in my post that I had exhaustively searched thru reams of evolutionary literature for months and months, eating little and sleeping less, in order to find the answers I seek. B/c it really seems to me like I remember saying sthg along the lines of: Here's something about which I'm fairly curious. I am very skeptical (no, really?) but really would like to know if anyone reading this can furnish an example of a mutation...

Call me lazy, that's cool. If you are intimately familiar with talk.origins, maybe you could give me the best, most relevant articles, or just summarise and paraphrase that which comes to mind. If you can fulfill the categories requested here, then we can dig yet deeper. If you can't, well, it stands demonstrated that you hold to evolution by faith absent a good answer to the question.

Peace,
Rhology

Rhology said...

hey CD,

By "information" I mean that DNA carries coding that leads to specified, complex life. DNA could carry nothing but junk that would lead to non-life. DNA is just a combination of chemicals and amino acids; put a random assortment of chemicals and amino acids into a vat and mix for 1 billion years and you won't get anythg out of it but a nasty smell.

Similarly, our common ancestor according to evolution was a very, very simple unicellular organism whose DNA, compared to the vast 100s of 1000s of different types of cells that make up just a human body, was very simple indeed. Where did the vastly more complex and specified information come from to get to where we are today in DNA?
Evolution's answer is mutation. That is taken on faith and faith alone, much like atheists accuse Christians of.

My question is designed to find out whether even the 1st step has been taken towards moving that question out of the realm of faith. 'Course, that's just a 1st step.

Strictly speaking any new mutation increases the information since it is a new sequence not contained within the previous sequence.

Well yes, but virtually all the time new mutations are detrimental to the organism.

Now then, you go into one interesting example which I guess I'll have to read up on, namely the pancreatic enzyme of the monkeys
As for viruses that cross species barriers, that is mostly tangential since viruses are only loosely described as a life form.
You go even further causing suspicion when you cite bacteria and drug resistance, though I specifically stated in my post the following: Just to forestall answers I've gotten in the past, I don't want to hear about your bacteria who grew resistant to antibiotics developed by humans, introduced by humans in a petri dish in a lab...

So, that's one possible example, I'll give you that. You kinda wasted your breath with the other 2 though.
And let me reiterate - just b/c the genome *changes* does not mean that it is advantageous (b/c usually it's not) and doesn't mean it increases specified and complex information in the genome, leading to a better system that could be acted on by natural selection.
Sexual reproduction - there is limited info within the DNA of 2 mbrs of the same species. Meld it together and you still have species-specific DNA info. The increase in beneficial info would have to come from elsewhere.

My criteria are based on the insistence FROM THE EVOLUTIONIST CAMP that intelligence could not possibly be responsible for what we see in nature. I'm just trying to be a good Darwinian acolyte and insist that, therefore, we make sure, dang it, that no intelligence be involved. Labs are designed by intelligence, so that's right out. Petri dishes - manufactured. No, this stuff needs to be out in the open so we can make sure it's 100% natural.

The probability of any particular mutation occurring are billions to one.

So that would be a "we don't have an example" for #5.

No one expects to see the same mutation occurring repeatedly.

But science is purported to be based on repeatable, testable results. This supports my contention that this is not science.

This is exactly what we do see, even in the moths and the bird's beaks that you choose to arbitrarily ignore for no good or even stated reason.

The reason I reject finch beaks is b/c when the rain returns, the finch beaks go back to where they were before the observation started. No divergence occurred.
The moths I reject b/c the entire scenario was fabricated. The moths don't come to rest on tree trunks; they hang out in upper branches normally. These moths were dead moths, pinned to the tree trunks.

Peace,
Rhology

chooseDoubt said...

Hi Rhology,

I get the impression that the only information you receive regarding evolution is from creationists. I know from our previous exchanges that you have reason to believe such information is not always honest. That is an understatement, the scale of which I hope you will one day be able to judge for yourself. To enable that judgement I recommend that you overcome your Dawkins allergy and read The Selfish Gene. I’ll even make you a deal to encourage you. You read that book and I will read any book that you request of me. We can discuss what we read in order to ensure that we are not missing the important points. How would you feel about this?

You said:
“DNA could carry nothing but junk that would lead to non-life. DNA is just a combination of chemicals and amino acids; put a random assortment of chemicals and amino acids into a vat and mix for 1 billion years and you won't get anythg out of it but a nasty smell.”

This is confusing abiogenesis, the emergence of life, with evolution. Evolution only applies once life has started. It’s even better to exchange the word “life” for the word “replicator”. Once any simple replicator emerges evolution then applies. Evolution describes the variety of replicators and their complexity. It does not describe their original formation, which appears to be far simpler than you may think.

DNA is just a combination of amino acids. We now know that these amino acids are formed by multiple natural and extremely common phenomena. They even form in space and what’s more they are even selected by radiation in space to the type (left) that forms the basis of all life on this planet. Beyond this we know of extremely common clays that catalyse the formation of complex molecules. We know of far more, but this is all abiogenesis and not evolution and we should not confuse the two. Suffice to say that with your barrel and a billion years then it is by no means certain that you would only get a nasty smell. With a billion billion barrels and four billion years not only would you get a nasty smell but, at least on this planet, you’ve also got billions of living things that can smell it. Abiogenesis only has to happen once. Once it has occurred, evolution as a process of random mutation and non-random selection clearly does explain the variety and complexity of the replicators we witness on this planet, including ourselves.

As for a common ancestor you have to define common to whom? Common to you and me and we can happily go back only 100,000 years (in fact, likely far less – read “The Ancestors Tale” for explanation) and we will share an ancestor. For humans and chimpanzees we can go back five million years. For humans, chimpanzees, and gorillas, 8 million and so on. What evolution says is that if we go back far enough then everything living on Earth shares a common ancestor and ultimately that ancestor will be even more complex than the first replicator. The first replicator would have been far simpler than a cell. Cells are incredibly complex collections of biological machinery, similar to vast communities of specialised bacteria. I don’t know how much you know about cells but it’s very likely that the average person’s idea of the complexity of processes going on in their entire body is radically less complicated than what is actually going on within any single cell in their body.

As you point out there are many different types of cell in the body and yet all of these cells contain exactly the same DNA. You ask where the vastly more complex and specified information came from to get to where we are today in DNA and the answer to that is evolution. It’s not faith. It’s a theory supported by absolutely all evidence we have and contradicted by none of it. It’s the reasonable thing to believe based on the evidence and the more you learn about it the more you are going to have to confront the fact that your creation theory is on the opposite end of the evidence spectrum. It isn’t just that there is no evidence for creation. It’s that the evidence flatly contradicts creation. That evidence comes from many sources and fields of study ranging far beyond biology. The only thing in support of your belief is your belief.

So, if your question is whether or not the first step has been taken to differentiate acceptance of evolution as a faith from acceptance of “god magically created everything as it is” as a faith then the answer is yes. So has the second step, the third, the fourth, the fifth and so on. Thousands of studies have been carried out that have returned evidence that supports evolution. Out of all the thousands of studies carried out not one of them has returned any evidence that contradicts evolution. How about with your creation theory? What studies have been undertaken and what evidence has been presented? None at all is the answer.

It doesn’t matter that most mutations will be detrimental to the resultant organism. Evolution has no problem with this. What matters is that some mutations make replication of the mutation more probable according to non-random selective pressures. Selection provides a successive filtering effect meaning that even tiny changes can over time add up to massive changes in gene frequency within a gene pool. And this is a process that is always in play. So instead of stirring a barrel we are stirring billions of barrels and skimming the top continuously. It is that which survives which forms the starting point of that which is then stirred.

Ignoring drug resistance is ruling a priori that important evidence must be ignored. The same arms race as we see between bacteria and antibiotics is exactly what has been going on between immune systems and bacteria. Bacteria are great for studying because of their rapid reproductive cycle which allows gene frequencies in a population change in time scales that we can study first hand. Using the fossil record and other sources we can do the same with other organisms but then we are explaining the past as opposed to observing change in action first hand. Of course, you also rule out such explanations on absolutely no stated grounds. Bird’s beaks have provided another form of first hand study and again you have arbitrarily ruled the evidence out. Why not just be honest and admit that you’ve already decided that the only evidence you’ll allow is the bible? That’s really the only position you can maintain since all the other evidence flatly contradicts the one piece of “evidence” you’ve determined must be true.

Rather than carry on writing arguments against your position which I feel confident you do not understand let’s try a different tactic. I pick The Selfish Gene for you to read and you can pick a book for me. At the very least we will better be able to argue against each other thanks to the increased exposure to the others background reading.

All the best,

CD

Rhology said...

CD,

After skimming your comment, I'd say you've made at least one interesting (and very possibly meritorious) point. I'll get to this in a few days.

Peace,
Rhology

rotsaP loeJ said...

Choosedoubt,
I'm not sure I understand the significance of a billion barrels over four billion years. The chances of a fellow leaping and not landing do not increase - even a little bit - if he leaps very slowly, nor if he tries a thousand times. Either we know things about the universe or we do not; if we know anything it is that something cannot come from nothing. So you have to believe without strict scientific proof in any case: either that self-existent chemicals mixed together can do things that are funky and impossible, or that a Creator-God can do things that are funky and impossible. In neither case does laboratory proof exist; in neither case is laboratory proof even admissible, any more than if you wished to know the outcome of Waterloo.

chooseDoubt said...

Hi rotsap loej,

The billion billion barrels over four billion years is a more accurate representation of the history of our planet than one barrel over a billion years. Yes that does change the probability. If I wish to receive at least one “tails” when flipping coins do I stand a greater chance if I flip 1 coin or a billion billion coins? Same for the emergence of a self replicator – stir one barrel or a billion billion barrels. But thanks for the straw man.

We do not know that something cannot come from nothing. We have a theory called the Conservation of Energy that states energy can neither be created nor destroyed but that applies to the confines of the universe we live within. We also already know that it is violated (temporarily) by virtual particles (quantum physics). So it is not a catch all. Saying that, I find the question of the origin of anything very interesting and so I won’t criticise you for stating it. But it has nothing to do with evolution or abiogenesis. When you suggest that it does you try to win a debate based only on an argument of ignorance. Neither of us knows how or even if nothing gave rise to something. It still has nothing to do with evolution.

So if you’d like to talk about the nothing to something conundrum (I have some thoughts on that and would be interested) let’s take that up elsewhere. But please don’t just throw every argument you have on anything into a specific question of a specific subject. It’s irrelevant and goes nowhere towards disputing my position – not even for you, if you are honest.

All the best,

CD

Rhology said...

Oh CD,

You lose points for saying:

We do not know that something cannot come from nothing.

That's brilliant. To be honest, I don't see why I shouldn't write off your entire worldview based on that gem alone.

We have a theory called the Conservation of Energy that states energy can neither be created nor destroyed but that applies to the confines of the universe we live within.

Which you know nothing about. You're grasping at straws here; you are defending your religion with nothing but faith.

We also already know that it is violated (temporarily) by virtual particles (quantum physics).

I don't see why that's relevant to the question, but if you mean that virtual particles could have caused sthg to come out of nothing, then:
1) that's not exactly nothing, is it?
2) you're appealing to imaginary things to make your absurd POV possible.

Neither of us knows how or even if nothing gave rise to something. It still has nothing to do with evolution.

Oh, leoJ rotsaP and I know that it wasn't like that at all. God created the universe. There was never "nothing." But in your view, we either have nothing poofing magically into something or an infinite universe, which is impossible. This is why I don't envy you.
However, you're right that it has little to do with evolution.
On the OTHER hand, so many atheists tie evolution so closely with their atheistic worldview that I'm tempted to ask why I should even consider evolution since the atheistic answers to the question of the origin of the universe are so abjectly hopeless. Almost, mind you - I wouldn't want to commit the genetic fallacy. Evolution by itself is perfectly pitiful on its own merits.

But yeah, I'd like to talk about the nothing-to-something conundrum, though it's been brought up on this blog before, recently. Maybe I'll post on it soon and we can talk.

Peace,
Rhology

chooseDoubt said...

Hi Rhology,

I really don’t want to get sidetracked into a discussion of a different topic but just to wipe a little of the froth from around your foaming mouth let’s waste a couple of minutes and see if it they calm you down.

Can you explain to me on what grounds the theory of Conservation of Energy has won your whole hearted allegiance which the theory of Evolution does not share? It’s just a theory, after all. I got the idea that seemed important to you.

You may also wish to re-read my previous comment in which I stated that this particular line of argument has no relevance to evolution and so was beside the point. I advise that you re-read my previous comment before further engaging in this celebratory masturbation. I was merely slightly indulged the off-topic arguments of ratsap loej. No reason to start throwing “write off your entire worldview” as reward for a courtesy shown to one of your other commenters.

My view is not that nothing poofed magically into something. That is far closer to your view than mine. Regardless, neither of us actually knows that it is impossible. If you really want to talk about nothing then I’d be happy to, but we’ll do it as a separate discussion to one concerning evolution. So let’s stick to evolution here.

The reason why so many atheists tie their atheism, or at least link it to evolution is exactly the same reason why so many creationists are investing so much time, energy, and money into trying to undermine evolution. As far as theories go it is the bible killer. It takes god out of the complexity of life. It removes the designer by showing how a simple process can so adequately account for our being here. It invalidates the soul and shows that tattered compendium of ancient ignorant mythology to be not just inaccurate but thoroughly ridiculous – less worthy or consistent than any fairy tale, for at least every fairy tale has a plot. It’s one of the best keys to unlocking the mind from the dull slavery of baseless and stupid dogma. They link to it for the same reason you and your ilk fight against it. It makes the truth obvious. All you have to do is understand it.

So please, if evolution is pitilful on its own merrits let’s hear those merrits. All I’ve heard so far is “something can’t come from nothing”. Stick to evolution’s merrits and before long there’s a good chance you’ll understand.

Don’t worry – you’ll get there. You’re a defender of fairy tale, a champion of nonsense – and you know it. It’s just taking a while for you to accept it – to admit it to yourself and those around you. You’ve invested so much in being wrong.

All the best,

CD

John Morales said...

Kudos to Rhology for acknowledging he is aware of talk.origins.

I'd like to know where I said or implied in my post that I had exhaustively searched thru reams of evolutionary literature for months and months, eating little and sleeping less, in order to find the answers I seek.

Here, I'll save you a week or two:
http://www.talkorigins.org/origins/search.html

John Morales said...

Hint: at the search page, searching for "mutation information", I get
Results 1 - 100 of about 204 from www.talkorigins.org for mutation information

Top result of those 204?
CB102: Mutations adding information

So, that took... 0.23 seconds of search time, according to the page. Plus your typing.

Now you can read.

Billy said...

"I'd like to know where I said or implied in my post that I had exhaustively searched thru reams of evolutionary literature for months and months, eating little and sleeping less, in order to find the answers I seek."

As John Morales has pointed out, it hardly required you to give up eating and sleeping in order to find the answers that you seek.

Given that your time is so precious, it's interesting that you were prepared to give up that time to go through the "intelligent design" talking points that you regurgitated in your post.

That tells us something about your priorities, but nothing very surprising.

Billy said...

So on to the substantial questions. It seems there are a few points that you're unclear on:

"Evolution's answer is mutation."

No. Evolution's answer is natural selection. Mutation is one of the mechanisms which natural selection acts upon to produce evolutionary change.

"That is taken on faith and faith alone, much like atheists accuse Christians of. "

No. It was originally based on observed evidence in nature. Where do you think Darwin got the idea from in the first place? Since then, it has been supported by observations in nature and in experiment, as the TalkOrigins references make abundantly clear.

"Well yes, but virtually all the time new mutations are detrimental to the organism."

And natural selection will then act to weed out the detrimental mutation. THAT'S THE POINT OF THE THEORY.

"we make sure, dang it, that no intelligence be involved. Labs are designed by intelligence, so that's right out. Petri dishes - manufactured."

This is possibly the stupidest thing that you've ever written. While the environment in which the processes takes place will be designed, the processes themselves are not "designed". You are confusing the two, and I'm guessing that you wouldn't apply the same constraints to experiments in (for example) particle physics.

"The reason I reject finch beaks is... No divergence occurred. The moths I reject b/c the entire scenario was fabricated."

Yes it did, and no it wasn't. It seems you had the time to read Jonathan Wells, although not the research that Wells was referring to; once again, we can assume this tells us more about your priorities than evolution.

Of course, Talk Origins has more interesting material on finch beaks (http://www.talkorigins.org/faqs/wells/finches.html) and on Wells in general, which covers the "peppered moths" (http://www.talkorigins.org/faqs/wells/iconob.html#moths). This stuff is really easy to find, really easy to understand and exposes objections to these two examples for what they are - obfuscation.

John Morales said...

rotsaP loeJ:
I anticipate that in case of the moths R. would say that they represent mere natural selection

Secondly, doesn't 'useful' in the context of evolution entail some survival advantage?

To the first, evolutionary theory is based on change (mutation) combined with (natural) selection over time. This “mere natural selection” acts as a ratchet.
To the second, consider parasites. Harmful parasites often become more benign to their host over time. Consider symbiosis.

Rhology said...

Hey John,

Thanks, I'll take a look.
I've been busy elsewhere dealing with similar questions, so we'll see where this goes.
I was just given some other examples of this by a guy who claims he's had over 50 peer-reviewed publications. His suggestions, however, had serious flaws and so I don't know what will come of that.

And I'll get to the other stuff later, but let's be real here. Nat Sel is but part of the mechanism. Mutations are where it's at in this discussion, b/c nat sel acting on a single-celled organism (ie, the common ancestor of all life forms) won't do anythg b/c there's nothing for it to act ON. None of those organisms, without having been mutated in order to produce different phenotypes, are different enough for nat sel to find any advantages to select or disadvantages to deselect. Let's try to stay on target.

Peace,
Rhology

chooseDoubt said...

Hi Rhology,

Are you are really saying that there is no way natural selection can operate on single celled organisms? I’ll check that is what you’re saying before I answer that claim as I’m astonished to read it. Surely you’re not serious.

Regards,

CD

Rhology said...

Dang this stuff can be time-consuming!

Responded here.

Anonymous said...

it's of no consequence what causes the mutation, whether in a lab or in a natural environment as the same process is still occurring ie adaptation to an environmental pressure via mutation/natural selection

if it is beneficial to survival in response to that pressure, then it is beneficial full stop. it's not as if eg a bacterium is aware that it's in a lab, all it responds to is the environment it is placed into.

there are plenty of natural pressures that will cause mutation (beneficial ones will allow adaptation via natural selection) that can also be used in a laboratory setting anyway eg heat, light, radiation, energy source etc etc.

if it survives, the change in information, whether by mutation of the original gene or in duplicate copies has increased the information. In some cases the original 'information' may no longer be kept as it is not useful to do so, in other cases it will be.

the whole point of adapatation is to deal with new pressures on the organism that it may never have experienced before - so therefore, if it has never experienced the pressure before, it does not matter whether it comes from a laboratory setting or a natural setting, as it is still unfamiliar to the organism.

Rhology said...

Hi Anon,

the same process is still occurring ie adaptation to an environmental pressure via mutation/natural selection

By removing the scenario into a lab, you're assuming without evidence that this would be adaptation to "environmental" pressure. The environment has radically changed in that case.

it's not as if eg a bacterium is aware that it's in a lab

True, but I'm not claiming that's the important factor. I'm concerned about the removing of all the influences that would normally be present in an organism's normal habitat. That's not recreatable in a lab.

Peace,
Rhology

Billy said...

"By removing the scenario into a lab, you're assuming without evidence that this would be adaptation to "environmental" pressure. The environment has radically changed in that case."

It doesn't matter where the environment is, it's still an environment. Your "argument" against laboratory experiments is therefore no argument at all.

"I'm concerned about the removing of all the influences that would normally be present in an organism's normal habitat. That's not recreatable in a lab."

And that's the point. You seem to have missed a key part of the scientific method - I urge you to read more about the hows and whys of experimentation, particularly the reasons why one has controlled experiments.

I continue to find it interesting that you firmly believe that a) your questions have not been answered (when as far as I can see, they have been), and that b) despite your admitted lack of knowledge, you have somehow managed to uncover the "truth" about evolutionary theory that 150 years of science - both observation and experiement - has failed to uncover. The mind boggles.

Rhology said...

It doesn't matter where the environment is, it's still an environment.

yes, it's a LAB environment, where CONTROLLED CONDITIONS exist. So I become suspicious when lab results like this bear out the evolutionary assumptions. You're loading the bases for your own side, and I don't think it's unfair to ask that studies be done in the environments in which this nat sel and mutation stuff was supposed to have taken place in order to produce the variety of life we see today. None of that stuff occurred in a lab, did it?

particularly the reasons why one has controlled experiments.

Yes, I know WHY, but in this case we're trying to repeat what happenED. And whatever happenED did not happen in a lab.
I thought your case was for natural selection acting on mutations. As you're proposing, it's artificial selection acting on mutations, some of which were forced by the observer.

despite your admitted lack of knowledge, you have somehow managed to uncover the "truth" about evolutionary theory that 150 years of science - both observation and experiement - has failed to uncover. The mind boggles.

It boggles my mind as well how willfully blind so many otherwise smart people are to this. Why *I* see it and many others don't, I'd have to attribute to God's grace.
Normally, one would think that the rationally superior position wouldn't have to resort to loading the die in its own favor in order to win the argument.

Peace,
Rhology

John Morales said...

Rhology,

You're not getting Billy's point.

The environment refers to the totality of surrounding conditions with which an organism interacts.

Organisms respond to their environment (whether it's natural or artificial) according to their nature.

Billy points out that it's unlikely that there're response mechanisms that distinguish between man-created and natural environments, and accordingly man-created environments can still elucidate the mechanisms organisms employ.

John Morales said...

Re my last post:

Note that your skin experiences the effects of UV radiation the same way whether the source sunlight or a tanning lamp.

Your respiratory system will show the same symptoms whether you're on a mountain or a hypobaric chamber.

In fact, your respiratory response will be the same whether you're underwater in a bathtub or a river.

Anonymous said...

yes, it's a LAB environment, where CONTROLLED CONDITIONS exist. So I become suspicious when lab results like this bear out the evolutionary assumptions. You're loading the bases for your own side, and I don't think it's unfair to ask that studies be done in the environments in which this nat sel and mutation stuff was supposed to have taken place in order to produce the variety of life we see today. None of that stuff occurred in a lab, did it?

particularly the reasons why one has controlled experiments.

Yes, I know WHY, but in this case we're trying to repeat what happenED. And whatever happenED did not happen in a lab.
I thought your case was for natural selection acting on mutations. As you're proposing, it's artificial selection acting on mutations, some of which were forced by the observer.


laboratory controls exist so that the only variable affecting the results is the experimental variable (eg a drug or food source etc) - ie not the human action.

The idea of a laboratory experiment is to model a particular condition or conditions of nature. it will never be perfect in this regard, however, it is not meaningless either.

Out of interest do you or have you ever taken any medication (even just aspirin for example? Have your relatives? Drug discovery goes through the similar experimental procedures i.e. testing on a model of the disease eg cats genetically predisposed to blindness models particular diseases that occur naturally in humans. Obviously not every drug is 100% effective due to the limits of time and completeness of research, as well as the model not being a 100% representation of the natural occurence. But if laboratory experiments can't model nature at all, you would expect the effectiveness in humans to be 0% right? In which case why did you take the medication, as surely you would have expected it to be completely ineffective if you think a laboratory experiment can't model nature at all?

as for loading the bases - if all the experimenter did was change a variable such as a food source compared to the control population then let the experiment take its course, then what exactly did he/she do to bias the results, given the aim was purely to find out what happened in a changed environment? Artificial selection relies on the experimenter selectively picking out the adapted organisms and discarding the less fit organisms then allowing only the ones with the adapted characteristics to breed. Natural selection simply lets the study population 'free run' to do this of its own accord.

Rhology said...

What I'm trying to get at here is not:
-can labs set up decent experiments to test the variable?
-can we repeat stuff over and over again to see what works and what doesn't?

I'm trying to point out that, if you think about it, we cannot recreate with ANY reliability AT ALL the supposed conditions of Organism X's habitat back in the day. We can guess at the conditions and all the variables that Organism X might have encountered. We can try to find out by studying the geological strata and other animals and plants that we THINK might have lived at the same time. But in the end, WE DON'T KNOW. That's the point of Henry Gee's In Search of Deep Time. I would recommend it. (He's a staunch evolutionist, BTW.)

So, run all the lab experiments you want. You can't get close to recreating what supposedly happened all those millions of yrs ago.
Even experiments run in the natural environment, where Organism X lives now, won't cut it, but they're closer. If you're looking for credibility, start there, not in the lab.

See, we're trying to test what happen***ED***, not what happen***S TODAY***. Nobody is disputing that. I'm disputing that evolution is how the variety and complexity of species we see today cAme about. Came, not comes.

John Morales said...

Rhology, your point is clear.

1. I'm trying to point out that, if you think about it, we cannot recreate with ANY reliability AT ALL the supposed conditions of Organism X's habitat back in the day.

2. So, run all the lab experiments you want. You can't get close to recreating what supposedly happened all those millions of yrs ago.

Your claim of no reliability at all seems rather absolute. Were the laws of nature somehow different back then? If not, the fundamental processes that apply today applied then.

I note you don't dispute that adaptation and genetic change/drift is occurring today, and has been extensively documented.

See, we're trying to test what happen***ED***, not what happen***S TODAY***.

Yes, we get it. You don't seem to get that experiments attempt to elucidate mechanisms and advance theory.

The more cogently you argue, the further you drift from your original tone.

Congratulations.

Anonymous said...

"By removing the scenario into a lab, you're assuming without evidence that this would be adaptation to "environmental" pressure. The environment has radically changed in that case."

yes, the environment changes in nature too - that's one of the reasons why evolution occurs as selective pressures change. environment refers to a creatures environs environments are never static in nature, hence why lab experiments observe what happens when the environs change as a reflection of natural processes. the researcher doesn't cut up the genome and rearrange it to deal with the changes - the population either evolves to cope or dies. same as nature.

Out of interest, consider the following scenario - a rat (A) is born in an animal facility and kept in a lab. it is kept on a 12 hour light/dark cycle. it is fed standard food and water.

a rat (B) is a wild rat, that lives according to sunlight/darkness, eats what it can scavenge for etc etc

is rat A therefore intelligently designed, and rat B a natural rat, even though they are still exactly the same species?

Apply the same thinking to a bacteria population. now, is the bacteria population intelligently designed, or merely an example of the same thing in a changed environment?


"it's not as if eg a bacterium is aware that it's in a lab

True, but I'm not claiming that's the important factor. I'm concerned about the removing of all the influences that would normally be present in an organism's normal habitat. That's not recreatable in a lab."

bacteria are found everywhere, from the gut, to skin, to the oceans etc - there is really no such thing as a 'natural habitat'. many creatures can survive in a variety of habitats, or can survive when their habitat changes. as long as your basic requirements are met eg energy source, vitamins, minerals, air etc you can survive a variety of conditions. this is exactly the same as for bacteria (or any other species). plus the researcher has to obtain the original bacteria from somewhere - where do you think this comes from if not nature? it's not as if the bacteria are built in a lab from scratch (although you never know in a few years time)

Anonymous said...

"Nat Sel is but part of the mechanism. Mutations are where it's at in this discussion"

nope - nat selection acts on any source of variation (it also acts phenotype not genotype). without nat selection you just have noise. nat selection provides order

eg endosymbiosis is a variation that accounts for features such as chloroplasts and mitchondria in eukaryotic cells that nat selection can act on

"See, we're trying to test what happen***ED***, not what happen***S TODAY***. Nobody is disputing that. I'm disputing that evolution is how the variety and complexity of species we see today cAme about. Came, not comes."

this is an odd viewpoint - why can it happen now but was not possible in the past? did evolution never happen prior to 1859 when OOS was published?

the theory of evolution makes testable predicitions - if certain predictions turned out differently the theory would be dead in the water.

eg if we ever find an animal that doesn't use the universal genetic code, it poses problems. so every new species discovery is a test of the theory

if there had been no universal code for replication, the theory was dead. the universal code was actually assumed prior to its confirmation, based on evolutionary theory.

if we ever find mammalian fossils in the cambrian, precambrian, ordovician or silurian deposits, the theory is dead in the water

as evolution predicts nested hierarchies (groups within groups),
if we ever find fossils with transitional features between birds and mammals, game over for evolutionary theory

if there had been no chromosome fusion discovered in the human genome (chimps have 24 pairs of chromosomes, we have 23) again game over (it had to be a fusion as a duplication in chimps would have been detrimental to reproductive success due to the deleterious effects these have, and a deletion in humans would have killed the species off due to the removal of so much genetic info)

if radioactive decay rates of certain elements were ever seen to significantly change under any conditions it would pose severe problems (i saw you argue that these things were not designed as clocks - protons never had MRI studies in mind, but they seem to be pretty handy for that, so just because something was not 'designed' for a particular use doesn't mean that property cannot be exploited for our information).

your core argument seems to be if a human was not there to document/witness it, it cant be certain (which is actually true, but there comes a point where the convergent results of independent studies stop being a coincidence), but if you apply that same idea to everyday life you'd be thought of as insane - eg if a cat is asleep in one corner of a room, you close the door, then when you open it 5 minutes later it's asleep in the other corner.

you didnt see it happen, but you'd assume it got up and walked there wouldn't you? another alternative would be some supernatural force allowed it to fly around the room then gently placed it down in the other corner - no human was there to witness what happened, so which explanation do you choose and why?

Rhology said...

Hi Anonymous,

I'll assume you're both the same person. Next time just choose a random name (like "Bob" or something) so I can distinguish. Thanks.

the environment changes in nature too

Exactly my point. The lab can't replicate that to reflect the pressures and changes of the environment. Not all of them. It's not even close.

rat A vs rat B

1) Yes, they are both intelligently designed, b/c evolution (TOE) is bunk.
2) But you're asking about RIGHT NOW. Your proposed rats are irrelevant. I'm asking about testing nat sel in NATURE.
3) If you don't have NATURE, you don't have NATURAL selection.
4) I know why you're not following the obvious here, but it's not reasonable to conclude that TOE is correct and that all your testing confirms it and THEN go to the evidence to cobble it together to fit.

bacteria are found everywhere, from the gut, to skin, to the oceans etc - there is really no such thing as a 'natural habitat'

The gut, skin, the oceans - those would be natural environments.
Petri dishes - those would NOT be natural environments.
BTW, has anyone ever observed a bacteria, even in a Petri dish, become sthg other than a bacteria?

plus the researcher has to obtain the original bacteria from somewhere - where do you think this comes from if not nature?

Precisely! And then he puts it somewhere ELSE, runs experiments on it in a scenario that would NEVER occur in the organism's natural environment, and then claims that this helps confirm sthg about the way that life's variety evolved in the past. Life's variety didn't evolve in a Petri dish.

without nat selection you just have noise. nat selection provides order

Philosophically, this is pretty laughable. A blind, undirected process that provides order?

why can it happen now but was not possible in the past? did evolution never happen prior to 1859 when OOS was published?

1) Evolution as you describe it never happened. (Hey, YOU brought it up!)
2) You ASSUME that what is happening now (scarce as the evidence you can bring may be) happened prior to 1859. I don't see why it's unreasonable to question that assumption. That's one reason why all this triumphalistic trumpeting of "We have the proof!!!" is laughable to me - it's based on so many assumptions that it certainly strains credulity.

the theory of evolution makes testable predicitions - if certain predictions turned out differently the theory would be dead in the water.

Its most fundamental predictions have never been observed, though. Given that, why not remain agnostic at minimum?
For example - no one has ever observed an organism evolve into another. Finch beaks don't count. Bacteria that evolve to resist antibiotics (and then die en masse when reintroduced into their original environment) don't count.
No one was there to observe how the fossil record actually came to be the fossil record. Fossils' primary function are not to tell time or tell evolution. They're there b/c they're skeletons of dead animals, and a LOT has happened since they died. That's Henry Gee's whole point in In Search of Deep Time.

if we ever find mammalian fossils in the cambrian, precambrian, ordovician or silurian deposits, the theory is dead in the water

1) You mean, MORE dead in the water than it already is.
2) I am supremely confident that the keepers of evolutionary orthodoxy will very possibly suppress any dissent from ev orthodoxy that such a discovery might produce.

as evolution predicts nested hierarchies (groups within groups),

There is widespread confusion among the evolutionary camp as to taxonomy and classification.

if we ever find fossils with transitional features between birds and mammals, game over for evolutionary theory

Why? You'll just come up with some other fairy tale to describe how it REALLY happened.

if there had been no chromosome fusion discovered in the human genome

I don't see why.
At best it would put a kink in the modern ideas of the origin of homo sapiens, which is hardly a nail in the evolutionary coffin, ISTM.

if radioactive decay rates of certain elements were ever seen to significantly change under any conditions it would pose severe problems

This is another massive assumption:
1) that these decay rates have always remained steady for millions of yrs;
2) that you know how much decay was already present at the "beginning" when the rock was "formed" in its current state (whatever all that means).
You don't know. You ASSUME all of this, and it leads you to ASSUME you know the age of the earth and rocks.

i saw you argue that these things were not designed as clocks - protons never had MRI studies in mind, but they seem to be pretty handy for that

No argument about that, but I do argue about these other things. Arguments to sustain these 2ndary effects are required.

your core argument seems to be if a human was not there to document/witness it, it cant be certain

No, I'm applying SCIENTIFIC RIGOR to these questions, using your own standards to judge your position.
The main way I know this stuff is bunk is that the Bible says it is, but I've also happened to find huge assumptions and inconsistencies in your own arguments.

another alternative would be some supernatural force allowed it to fly around the room then gently placed it down in the other corner

Yes, that's true.
But there's a big difference between the two scenarios. The God of the Bible has revealed how it all went down, explicitly. He doesn't move cats around, but He does create the universe and life.
And there's no logical inconsistency in either scenario of the cats - either one is logically possible.
However, evolution is at least doubtful given its errors and inconsistencies and huge assumptions.

Hope that helps.

Peace,
Rhology

Rintintin said...

# has been observed in an organism NOT IN A LAB (b/c that would inject intelligence into the equation, and I'm after full nature here),
# has increased the USEFUL information in the genome,
# has been BENEFICIAL for survival in the organism's natural habitat,
# which occurred without ANY human intervention whatsoever,
# and which has been observed repeatedly.

hi Rhology

I thought Id answer your points made here, plus ask a few questions of my own.

1) By what mechanism do you feel human 'intelligence' or the fact that a human possesses a high level of cognitive function would be able to alter an organisms genome in a controlled lab experiment? Also, do you not consider humans to be part of nature, since we do not possess supernatural powers like whatever is doing the 'designing' that ID proponents talk of? How do our 'intelligent actions' affecting evolution differ from say a bird, which although not at the same level of brain capacity as a human, can still make intelligent decisions eg with what beetles or bugs that it wants/likes to eat - is this not equally 'artificial selection' by your defintion given that an organism with a degree of intelligence is doing the selecting? Do you consider fish in a tank to be unnatural products of intelligent design, even though a tank is simply a smaller model of the oceans or a river?

2) How do you define 'information'? Is smoke from a lightning strike on a tree intelligent design as it gives us information that there may be a fire? Also, evolution does not necessarily need to generate more 'information' as some adaptations can involve loss of functions that are not useful in a particular environment (eg cave salamanders no longer have eyes) but this has the advantage of pressing less of a metabolic demand than organisms supporting unnecessary extra capabilities.

3) The idea of evolution is that it is response to a change in habitat (even if that change is only slight, it can have great effects) rather than acquiring traits that the organisms in question would like to have in a static environment.

4) See 1 - humans are part of the natural world and our actions have evolutionary effects the same as any other organism. Humans are not excluded as some special case in evolution, and as I have said nor do we possess supernatural powers of any sort. even the materials (eg drugs) we produce by synthetic processes are still made from naturally occuring chemicals.

5) Chloroquine and pyrimethamine resistance in malaria parasites has been observed repeatedly in numerous parts of the world and can be linked to various point mutations. resistance to atherosclerosis and HIV have both been observed in humans as a result of mutations (CCR5 delta 32 is a 32 base pair deletion that confers HIV resistance).

upon reintroduction into a petri dish full of the original kind of bacteria, died en masse (though no one ever mentions that part).

That's not surprising in the slightest - the resistance to eg antibiotics carries an increased metabolic demand to synthesise the necessary protein(s). As there is no longer selective pressure for drug resistance, the wild type (bacteria without the resistance mutation(s)) would be naturally selected for as they require less energy to be directed to unnecessary processes and are therefore 'fitter' for the drug free environment. Additionally, the fact that you know this happened means that obviously in the original papers people must have published this information, so why do you feel people are trying to cover something up despite the fact that they have made it open knowledge to anyone with access to journals?

I don't want to hear about peppered moths or finch beaks.

Why is that?

That's just science. I want to see if evolution fits the bill.

well, evolutionary theory allows for the making of testable, falsifiable predictions, so yes it is science.

Rhology said...

Hi RTT,

Thanks for your patience. I've got a queue, and I'm behind in it, obviously!

1) By what mechanism do you feel human 'intelligence' or the fact that a human possesses a high level of cognitive function would be able to alter an organisms genome in a controlled lab experiment?

Well, I'm just using examples given to me by Darwinians. By causing mutations and then manipulating the environments to accentuate the differences so as to cause the unmutated to die out, etc.
What I dispute is that this is valid demonstration of the explanatory power of Darwinian mechanisms to have been the cause of the variety of life we see today. It's so disanalogous in the most important areas in question; such examples beg the questions.

do you not consider humans to be part of nature

Sure. And they're INTELLIGENT. Not blind. They direct things.
See how far you've strayed from the Darwinian mechanism? You might as well be an ID proponent by now! Theistic evolution or something, at minimum.

we do not possess supernatural powers like whatever is doing the 'designing' that ID proponents talk of?

ID does not necessarily postulate a supernatural force. It postulates a designer of indeterminate bkgrd and definition and correctly recognises that hypothesising the identity of said designer is beyond the realm of science. I don't understand why that's so hard to understand, but then again, naturalists love to dress up metaphysical assertions in the royal robes of "science", so it shouldn't surprise me.

a bird... can still make intelligent decisions eg with what beetles or bugs that it wants/likes to eat

This is so far removed from the question that I don't see its relevance.

Do you consider fish in a tank to be unnatural products of intelligent design

Well, let's think about it for a second.
How is this even a question? It's unbelievable!
Did a fishtank develop thru wholly natural processes? Or did an intelligence design it?


2) How do you define 'information'?

It's specified, it's complex, etc.
It is orderly; a DNA molecule with useful information produces an organism that functions, rather than constantly causing spontaneously-aborted blobs of tissue that never even developed into a working cell.
The difference between a blog comment from a Darwinian to a creationist fundy as opposed to dfjn,.p[i,,adsfkjadpio223782';lmafdd

Is smoke from a lightning strike on a tree intelligent design as it gives us information that there may be a fire?

No.

evolution does not necessarily need to generate more 'information' as some adaptations can involve loss of functions

Your obligation is to produce pathways that lead from unicellular organisms to the complexity of today's organisms. Don't insult my intelligence and talk about LOSS of complexity and functionality. It's a waste of time.

3) The idea of evolution is that it is response to a change in habitat (even if that change is only slight, it can have great effects)

It may have great effects, but it's a question-begging assumption to assert that it leads to lizards changing into birds. Such has not been observed but only guessed-at.


nor do we possess supernatural powers of any sort.

Nor is any required to shoot down Darwinian mechanisms.
We ARE intelligent.


5) Chloroquine and pyrimethamine resistance ...confers HIV resistance).

Congratulations, but I happily grant such things.
And they don't get past several of the conditions I laid out above anyway.

why do you feel people are trying to cover something up despite the fact that they have made it open knowledge to anyone with access to journals?

I'm not necessarily talking about the original researchers, obviously (else how would I know it?).
I'm referring to the question-begging Darwin apologists with whom I often talk.

I don't want to hear about peppered moths or finch beaks.
Why is that?


I wrote something up on finches here.
Just for you, in fact! :-)

evolutionary theory allows for the making of testable, falsifiable predictions, so yes it is science.

It doesn't OBSERVE the very questions at hand. The predictions it is able to test are willingly granted, by me and others. They're not the question.

Peace,
Rhology

Rintintin said...

Hi RTT,

Thanks for your patience. I've got a queue, and I'm behind in it, obviously!


no problem, i understand that you obviously get a reasonable number of posts to answer as well as presumably having a day job to deal with!


1) By what mechanism do you feel human 'intelligence' or the fact that a human possesses a high level of cognitive function would be able to alter an organisms genome in a controlled lab experiment?

Well, I'm just using examples given to me by Darwinians. By causing mutations and then manipulating the environments to accentuate the differences so as to cause the unmutated to die out, etc.
What I dispute is that this is valid demonstration of the explanatory power of Darwinian mechanisms to have been the cause of the variety of life we see today. It's so disanalogous in the most important areas in question; such examples beg the questions.


I think you have to separate slightly the evidence for common descent and mechanisms of evolution - scientists are certain evolution did happen (for reasons I can expand on if you like), what is more open to debate are the specific mechanisms that drive evolution (although obviously natural selection and mutation are considered 2 major players in this).

In lab expts where genomes are being manipulated, the researcher's presence as a confounding variable is controlled for - the idea is to find what happens in mutated v unmutated organisms, or in a static vs variable environment for example. Any given population of organisms whether they be human, bacteria, rat or whatever has a basic set of minmimums for survival - after all a human in Britain can survive in America or Sweden, or in a house, tent or a mudhut equally well in either natural or artificial environments. This is no different to taking bacteria from nature and putting them in a dish (in fact, leave a medium plate out long enough and the bacteria will find their own way there...). Changing the environment eg such as sugar source is simply trying to model a change in environment in 'the wild'. There is simply no way we can examine genomes or work out what they do without a human coming in contact with the organisms to be studied, which is covered by the use of controls - also, remember these are the same experiments the likes of Mike Behe take data from to infer design (but more on that in a second).

do you not consider humans to be part of nature

Sure. And they're INTELLIGENT. Not blind. They direct things.
See how far you've strayed from the Darwinian mechanism? You might as well be an ID proponent by now! Theistic evolution or something, at minimum.


Every living organism directs what happens in nature via their interactions with each other. Humans are part of that - what i want to know is how the specific trait of human 'intelligence' (and remember many animals could also be described as intelligent) simply being near an organism can alter a genome in a directed manner, or how our selection differs from any other organism being responsible for the selection?


we do not possess supernatural powers like whatever is doing the 'designing' that ID proponents talk of?

ID does not necessarily postulate a supernatural force. It postulates a designer of indeterminate bkgrd and definition and correctly recognises that hypothesising the identity of said designer is beyond the realm of science. I don't understand why that's so hard to understand, but then again, naturalists love to dress up metaphysical assertions in the royal robes of "science", so it shouldn't surprise me.

It doesn't but if one posits a natural designer, this is a testable proposition, and we should be able to detect its presence today, as various adaptations occur that they feel evolutionary science can't explain eg with administration of anti-malaria drugs - as we can find no natural designer, this leaves only the supernatural as a choice, which you correctly point out is untestable, plus the 'unknown designer, working at unknown time, by unknown mechanisms in unknown places' is a cover all for any scenario and therefore cannot be considered scientific. This means that they have provided absolutely nothing different from 'we don't know how this happened' since they have made absolutely zero +ve claims for design such as a mechanism or designer, except they have decided to tag a fancy name to it and pass it off as a scientific theory.


a bird... can still make intelligent decisions eg with what beetles or bugs that it wants/likes to eat

This is so far removed from the question that I don't see its relevance.

because this will have an effect on the population via which members live/die and therefore which traits get propagated - much the same way as human selection. Again, Why is human selection considered separate in your eyes from selection by any other organism with a degree of intelligence/decision making ability?

Do you consider fish in a tank to be unnatural products of intelligent design

Well, let's think about it for a second.
How is this even a question? It's unbelievable!
Did a fishtank develop thru wholly natural processes? Or did an intelligence design it?


That doesnt answer the question, Im talking about the fish themselves not the tank - the fishtank is designed as a model of the normal environment for fish - if I take fish from an ocean or river where they were born/grew naturally without any intervening human hand, then transport them to a tank which is a smaller/basic version of their environment, do they thus sudenly become products of intelligent design the same way as you are arguing bacteria do in a petri dish in a controlled experiment? And again, these are the same experiments Behe is using to make his claims for design, which you are supporting - so either you reject Behe's claims also and accept that we can know nothing from lab experiments, or you accept that lab science is a valid way of modelling processes in the natural world


2) How do you define 'information'?

It's specified, it's complex, etc.
It is orderly; a DNA molecule with useful information produces an organism that functions, rather than constantly causing spontaneously-aborted blobs of tissue that never even developed into a working cell.
The difference between a blog comment from a Darwinian to a creationist fundy as opposed to dfjn,.p[i,,adsfkjadpio223782';lmafdd


I'm not sure if this is the answer to the question you are asking or not as again those terms S and C are slightly vague: information is really an emergent property that we see with the benefit of hindsight - the problem with ID's ideas and uses of probabilities regarding genetic information is that they are looking at the situation post-hoc, and treating any gene, system or series of mutations as 'the one true sequence'. Behe even brings up this caveat in Behe and Snoke (2004) then promptly ignores not only his own statement but evidence of many examples where a variety of different sequences can confer very similar properties to a gene or protein sequence! It also relies on the idea that cumulative changes can't account for what we see with hindsight. Taking IC systems as examples of SC as Behe/Dembski do, what they argue is (there are numerous variants on how they define this, so its very hard to pin them down to one given the continual goalpoast shifting) that "

A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system (Dembski).

Unfortunately none of the systems they give fall into this - some e.g.s:

The mammalian blood clotting cascade - knockouts of some of the various genes in the cascade don't affect clotting ability, there are also examples in nature of organisms with less than the number of components in the mammalian cascade (whales, pufferfish). Also, components of this cascade perform other functions apart from blood clotting, so they are hardly well matched (seeing as some are redundant), specified (as they perform more than one function) or irreducible (as removal of parts doesn't break the system).

The flagellum - again, not well matched as there are thousands of flagellae, and some are missing proteins that are present in others. Again many of these genes/proteins have functions elsewhere in the cell as part of other systems. there are also sub parts of the flagellum that act as functioning systems in their own right.

Malaria - Behe states that 2 specific simultaneous mutations on two separate gene loci are needed for CQ drug resistance. First of all, there are many double point mutations that confer this trait. Secondly, there are examples where a single point mutation in one locus is enough to confer resistance. And 3rd again ignores the possibility of cumulative selection via selective steps (I know for a fact that there is data showing this).

Behe also admits to ignoring circuitous routes for any given IC system as they are 'improbable'. Evidence given for claim? None.

Additionally, none of their arguments are new - AG Cairns and HJ Mueller (amongst many others) proposed these ideas well before Behe, and Ludwig von Bertalanffy specifically applied it to biological systems (not that this has ever received any acknowledgement from Behe who states he is the first to apply it to biology!)


evolution does not necessarily need to generate more 'information' as some adaptations can involve loss of functions

Your obligation is to produce pathways that lead from unicellular organisms to the complexity of today's organisms. Don't insult my intelligence and talk about LOSS of complexity and functionality. It's a waste of time.

I thought it was worth pointing out, since Behe complains continually about systems that haven't shown complex changes as falsifying 'Darwinism' - it is not always necessary. I will however address your point in a new post as this one is getting quite lengthy already - although I would recommend Sean Carroll's book explaining developmental biology as a good starting point if you have genuine interest in this sort of thing.

3) The idea of evolution is that it is response to a change in habitat (even if that change is only slight, it can have great effects)

It may have great effects, but it's a question-begging assumption to assert that it leads to lizards changing into birds. Such has not been observed but only guessed-at.

Funnily enough as we dont live hundreds of millions of years, Id be surprised if anyone claims to have watched evolution as it happened. There are many preocesses in science not directly observable due to distance of time (evolution), distance in space (eg distant stars and planets), difficulty of access (eg the Earth's core) etc. furthermore, biology is not the only research disqualified under the criterion of indirect observation - history, linguistics, epidemiology, virology, astrophysics


nor do we possess supernatural powers of any sort.

Nor is any required to shoot down Darwinian mechanisms.
We ARE intelligent.


Again, other animals are capable of selection - you are trying to put humans on a pedestal above nature. How would a human presence in nature alter a genome in a directed fashion the way the designer is purported to?


5) Chloroquine and pyrimethamine resistance ...confers HIV resistance).

Congratulations, but I happily grant such things.
And they don't get past several of the conditions I laid out above anyway.


But on one hand you demand experimental evidence, then go on to state humans cannot do experiments because 'intelligence' somehow taints any experiment, even with proper controls in place! and I'll say it again for emphasis, these are the same experiments the ID crowd are cherry picking data from to make their claims.

why do you feel people are trying to cover something up despite the fact that they have made it open knowledge to anyone with access to journals?

I'm not necessarily talking about the original researchers, obviously (else how would I know it?).
I'm referring to the question-begging Darwin apologists with whom I often talk.


I assume you would describe me as a Darwinist, and I gave you an explanation of why that happens without a second thought, as would anyone with a little knowledge of biology. There is no great trick or cover up being played here - there is no conspiracy theory to oppress religion (around 40% of scientists follow a religion of some description after all). Unfortunately for biblical literalists, the natural world does not reflect the claims made in several parts of the bible.


I don't want to hear about peppered moths or finch beaks.
Why is that?

I wrote something up on finches here.
Just for you, in fact! :-)


haha, you're too kind :) - I posted an answer to that one earlier

evolutionary theory allows for the making of testable, falsifiable predictions, so yes it is science.

It doesn't OBSERVE the very questions at hand. The predictions it is able to test are willingly granted, by me and others. They're not the question.

As I explained many many fields of science/research rely on indirect observation, whether due to length of time, distance or ease of access. If you want to rule out evolution as a field of study for that reason, you can start by ruling out a heck of a lot of other research too if you are being consistent

if I have a theory and I want to test it based on what we already know, we can make a prediction about what we should find if our theory is correct, regardless if we are dealing with the distant past. Fossils are a good example of this: we have 2 creatures X and Y that we believe show a transition, and that these creatures were alive in a particular part of the world at particular times in history - if our previous studies are accurate and our theory is correct, we should expect to find fossils of creature Z showing morphology intermediate between the X and Y, in a particular geographical location in a particular rock. If we find this, it supports our hypothesis. As this has been done successfully on numerous occasions, you have two options - either the theory is accurate or numerous researchers have gotten extremely lucky on countless occasions.

anyway, have a read and respond at your leisure

Thanks

Rintintin said...

"there are also examples in nature of organisms with less than the number of components in the mammalian cascade (whales, pufferfish)."

sorry, that should have read 'in the human cascade', as whales are of course mammals :)

Rhology said...

Howdy,

A day job AND a night job, actually. Erf. But the night job is almost done!

scientists are certain evolution did happen

But I'm not. That's the big question at hand as far as I'm concerned.


the researcher's presence as a confounding variable is controlled for

I don't see how that could possibly be done. INTELLIGENCE is present. These lab expts at least partially support my position, and certainly support the ID position.

Changing the environment eg such as sugar source is simply trying to model a change in environment in 'the wild'.

But can't you see how there are so many myriad variables in the wild that a lab can't possibly account for them all?
Even in the Darwinian model, there's not just one "pressure" that moves evolution "fwd".
You have before you a virtually impossible problem in my estimation, and I'm glad I'm not in that same spot.

There is simply no way we can examine genomes or work out what they do without a human coming in contact with the organisms to be studied

1) Bummer for you. I guess there's no way for TOE to be scientifically verified.
2) I'm not talking about examination so much as the manipulation that goes on.

Every living organism directs what happens in nature via their interactions with each other.

Nobody is claiming that bacteria are intelligent. I'm talking about HUMAN INTELLIGENCE here. A statement like this is fairly disingenuous.

what i want to know is how the specific trait of human 'intelligence' (and remember many animals could also be described as intelligent) simply being near an organism can alter a genome in a directed manne

It's the MANIPULATION in expmts that concerns me.

It doesn't but if one posits a natural designer, this is a testable proposition, and we should be able to detect its presence today

Many people think that dark matter/energy are good naturalistic solutions for certain problems, and they can't detect either. Yet. Know your limitations.

as we can find no natural designer, this leaves only the supernatural as a choice

Of course, *I'm* not positing a natural designer. :-D I'm just talking about ID guys.

design such as a mechanism or designer, except they have decided to tag a fancy name to it and pass it off as a scientific theory.

There are some YECs that do that, but I don't call it a "scientific" theory.
And of course I don't think that "scientific" is necessarily equivalent to "truthful".

the fishtank is designed as a model of the normal environment for fish

All well and good, but
1) it's not the normal environment; so many factors are absent
2) the tanks are intelligently designed.


do they thus sudenly become products of intelligent design

Not the fish, but the tank.
And all subsequent expmts that could be performed would be tainted by ID.

these are the same experiments Behe is using to make his claims for design, which you are supporting

Gasp! His expmts deal with ID?!?!?!

Blood clotting, malaria

I'm not an expert on these so I have little more to say.

there are also sub parts of the flagellum that act as functioning systems in their own right.

Fine, but that's only a small part of the puzzle.
I want to see pathways from nothing to those subparts, then from those subparts to the flagellum. And explanations of what the organism was doing with those subparts in the interim, while the structures were transitioning from subpart to flagellum. What function did they perform? How did they confer extra fitness to the organism in that time?

Id be surprised if anyone claims to have watched evolution as it happened.

I've never heard that, either. But my problem is that science gets redefined when we're talking Darwinianism. Talk about shifting the goalposts! All of a sudden, this stuff doesn't need to be observed, it just needs to be guessed at given microevol and some fossils we think show a pattern.

How would a human presence in nature alter a genome in a directed fashion the way the designer is purported to?

Human expmtation injects INTELLIGENCE into a system that you're trying to prove occurs w/o INTELLIGENCE.
I don't know how to put it any more simply.

But on one hand you demand experimental evidence, then go on to state humans cannot do experiments because 'intelligence' somehow taints any experiment, even with proper controls in place!

Yes, I agree that you're in a really tough spot.
But it's of your own making; I say you should lie in the bed you've made.

There is no great trick or cover up being played here - there is no conspiracy theory to oppress religion

Honestly, it looks like you're totally wrong (and ignorant of occurrences of that exact kind) from my side.

Peace,
Rhology

Rintintin said...

But I'm not. That's the big question at hand as far as I'm concerned.

No disrespect intended, but you seem to have an unusual view of what does and doesn't constitute science.

I don't see how that could possibly be done. INTELLIGENCE is present. These lab expts at least partially support my position, and certainly support the ID position.

Presumably addition of say an experimental solution in your eyes is exptl. solution + intelligence, then you would have the vehicle (control) solution, which could be expressed as vehicle + intelligence


therefore if you see an effect in the exptl. group but not the control group, how can the mere presence of intelligence rather than the type of solution (let's say it's something natural like a type of sugar) be the factor causing the effect if intelligence is present in both experiments?

You also have a duty to explain experiments that fail to produce any effect in either group, or support the opposite of the predicted hypothesis if intelligence guides the outcome to the desired conclusion. You could also ask why our intelligence would direct the result of complexity, when surely it would be more worthwhile to take the approach of simplicity?


But can't you see how there are so many myriad variables in the wild that a lab can't possibly account for them all?
Even in the Darwinian model, there's not just one "pressure" that moves evolution "fwd".
You have before you a virtually impossible problem in my estimation, and I'm glad I'm not in that same spot.


Again you can argue the same point for any lab science - how are any findings applicable to the real world if lab science cannot model any natural process in its entirety?

There is simply no way we can examine genomes or work out what they do without a human coming in contact with the organisms to be studied

1) Bummer for you. I guess there's no way for TOE to be scientifically verified.
2) I'm not talking about examination so much as the manipulation that goes on.


1) or any other lab science - in fact why do experiments if intelligent presence is the directing factor? Simply being near say a sick patient should be enough to make them better if it is the intelligence rather than the experimental condition that directs the outcome.


Nobody is claiming that bacteria are intelligent. I'm talking about HUMAN INTELLIGENCE here. A statement like this is fairly disingenuous.

What about chimps and so on that could be considered to have at least a primitive version of many aspects of human intelligence?

And again, how do you account for experiments that fail, or support an alternative to a predicted hypothesis?

1. Conscious intelligent agents exist in the world.

2. These agents have causal and discernible powers.

3. These agents use their powers to have discernible effects- including irreducible or integrated complexity, complex digital and sequence information.


This is a summary of what Stephen Myers feels is the reason to accept ID. As science would now like to identify a designer, the only designer discussed that falls under this bracket (as identified by IDists) are humans. yet ID does not conclude that humans designed the world's biodiversity.


It's the MANIPULATION in expmts that concerns me.

Again its an attempt to model conditions of nature.


There are some YECs that do that, but I don't call it a "scientific" theory.
And of course I don't think that "scientific" is necessarily equivalent to "truthful".


But it does imply a certain methodology has been used - ID wants to make at least a degree of allowance for non-natural explanations. This is like asking to play soccer with one's hands - it defeats the point of the enterprise.

the fishtank is designed as a model of the normal environment for fish

All well and good, but
1) it's not the normal environment; so many factors are absent
2) the tanks are intelligently designed.


So if I drop it back in its natural habitat after a few weeks in the tank does that mean the fish has gone from being a natural organism, to an intelligently designed one and back again?


do they thus sudenly become products of intelligent design

Not the fish, but the tank.
And all subsequent expmts that could be performed would be tainted by ID.

these are the same experiments Behe is using to make his claims for design, which you are supporting

Gasp! His expmts deal with ID?!?!?!

Not in the way you think - he doesn't suggest as far as I know that simply doing a lab experiment supports ID. Rather that some data produced by experiments cannot be accounted for by known evolutionary mechanisms.

Blood clotting, malaria

I'm not an expert on these so I have little more to say.


That's fine, but shouldn't you familiarise yourself with them if you agree that they support the presence of design in the world?


Fine, but that's only a small part of the puzzle.
I want to see pathways from nothing to those subparts, then from those subparts to the flagellum. And explanations of what the organism was doing with those subparts in the interim, while the structures were transitioning from subpart to flagellum. What function did they perform? How did they confer extra fitness to the organism in that time?


The problem here, as with Dembski, is that no matter how much detail I or anyone else gives, you will always demand more - basically demanding infinite levels of detail. Besides this, even if there is a lack of an evolutionary pathway, this still isn't support for ID, as ID has not provided any mechanisms, times/places or a designer to support design.

This article deals with flagellar evolution points worth noting: only 2 out of around 40 or so proteins are actually essential and unique (ie have no known homologues) to the system; other bacteria that don't have flagella possess some flagellar genes)

http://www.nature.com/nrmicro/journal/v4/n10/full/nrmicro1493.html - i think it is available for free, if not let me know and I can summarise it (as I don't want to break any copyright laws).

or you can read a discussion of it here:

http://www.pandasthumb.org/archives/2006/09/flagellum_evolu.html

I've never heard that, either. But my problem is that science gets redefined when we're talking Darwinianism. Talk about shifting the goalposts! All of a sudden, this stuff doesn't need to be observed, it just needs to be guessed at given microevol and some fossils we think show a pattern.

The idea of descent from a common ancestor can be used to generate testable predictions about what should be observed in nature if the idea is correct. If certain predicitions are not observed, or the opposite is observed, the theory is false.

So it can generate testable falsifiable predictions - how is this not science?


Human expmtation injects INTELLIGENCE into a system that you're trying to prove occurs w/o INTELLIGENCE.
I don't know how to put it any more simply.


see my first few points on this.


Yes, I agree that you're in a really tough spot.
But it's of your own making; I say you should lie in the bed you've made.


again, then how are experiments applicable to real world situations? Under your premise we can learn nothing, as 'intelligence' somehow taints all experiments. This means it is either impossible to support any hypothesis never mind whether it is for evolution or ID.


Honestly, it looks like you're totally wrong (and ignorant of occurrences of that exact kind) from my side.

I work as a biologist - Ive never heard of anyone I know being denied a position or promotion on the basis of their religious views. I've also never heard of anyone being forced to accept evolutionary theory in order to keep their job.

ID doesn't generate any data - why would you expect a researcher to get favourable treatment if they are doing something that by definition can't produce any results? Especially as in most cases they are being paid to do something totally unrelated to ID?