bob b, Re: 'Increasing Genetic Information'

sentientsynth

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Johnny said:
Indeed, and this is probably being done to some limited extent. I would imagine the problem with doing this in more advanced organisms is primarily analyzing and comparing genetic information. We have the ability to do the required genomic manipulation, but the analysis of the genomic changes--even with a completely mapped genome--would still be tricky.
Yes. It'd be slow, pain-staking work. What would Pehr Edman do? (WWPED?)

One would have to account for neutral mutations, regulatory changes, changing genetic domains, etc. etc. [snip] So it's not as easy as comparing gene-for-gene changes, we'd have to look at the big picture.
I see.

We're still working on the "big picture". As we move up along the chain of life, the interactions which control gross morphology become horribly tangled. We're still trying to figure why humans are the way they are, much less other species.
I bet it does get awfully hairy. Sounds very intriguing, though. Perhaps I should have remained a BIO major. NAh.....

Maybe by the time you finish your PhD this field will be picking up.
By the time I finish my PhD, humans will have devolved into puddles of slime. But seriously, I'm not sure if I'm going to go for a PhD. A MS will allow me to do the limited research that I've got my eye on currently (soil nitrogen-fixation). But maybe along the way I'll find the opportunity.

Nonetheless, we are beginning to see research like this emerging on a very simple scale. [snip] The interesting thing with this paper is that they actually expressed the proteins and showed that the receptor specificity increased as predicted. However, it was extremely simplistic and they only traced two specific mutations.
Still incredible, however "simple." And this is exactly the kind of research I'm interested in seeing. Well, I want to engineer a autotropic organism that uses carbon monoxide in respiration. Natural "scrubbers." Wouldn't that be neato?

I have to run to class,
You're still in the semester? We took finals last week.

I'll try and see if I squeeze something out of pubmed later ;)
Cool. If you find anything, let me know your keywords, K?


C-Ya Round,

SS
 

Johnny

New member
Mods, sorry about that double post. I clicked "Stop" before it went through and then resubmitted, thought my computer was just being fussy.
I bet it does get awfully hairy. Sounds very intriguing, though. Perhaps I should have remained a BIO major. NAh...
What is your major again? I know you've told me once, but that information was kicked out to make new room.
But seriously, I'm not sure if I'm going to go for a PhD. A MS will allow me to do the limited research that I've got my eye on currently (soil nitrogen-fixation). But maybe along the way I'll find the opportunity.
Ah I see.
Well, I want to engineer a autotropic organism that uses carbon monoxide in respiration. Natural "scrubbers." Wouldn't that be neato?
That would be amazing. I've always wondered how much research actually goes on in these fields, I'm sure there is a lot. It seems bacteria are capable of making just about anything an energy source, so why not use them to clean up after ourselves--maybe even create a usable biproduct in the process. But there are lots of people rabidly against bioengineering. Feh.
You're still in the semester? We took finals last week.
Yea(we have quarters), and unfortunately in the worst part of it. Four exams in the next eight days, followed by 5 cumulative finals and two practicals in a five day period. Good times.
 

One Eyed Jack

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sentientsynth said:
It seems like once we have a complete genome of a species, we could compare it to that of a "relative" species and see how we could make slight changes to convert the one to the other.

That's what they did in Jurassic Park -- made dinosaurs out of frogs. Unfortunately, they didn't figure in the ability of some amphibians to spontaneously change sex -- a trait which carried over to their genetically modified dino-descendants.

Funny thing about Jurassic Park -- I swear I read a short story (or maybe an excerpt from a longer story) in Read magazine back when I was in elementary school about the same subject -- using modified frog DNA to produce dinosaurs. This was like ten years before Jurassic Park was ever published. I wish I could remember the name of the article.
 

sentientsynth

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I thought they supplemented dino DNA with a small portion of froggy DNA, which happened to have a little bit of that "swingin' DNA" on it.
 

One Eyed Jack

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sentientsynth said:
I thought they supplemented dino DNA with a small portion of froggy DNA, which happened to have a little bit of that "swingin' DNA" on it.

Yeah, but I think they were using frog DNA as a template to begin with.
 

One Eyed Jack

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I could be wrong too -- it might just be an assumption on my part. It's been a while since I've read the book or seen the movie.
 

Stripe

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in jurassic park the dinosaur sequence was incomplete so they completed it with frog dna.
 

noguru

Well-known member
sentientsynth said:
I think I see what you're saying. You're saying that is wasn't a dog that became a horse. There was a common ancestor to both the dog and the horse which they both evolved from. Going from today's dog to today's horse is a different affair. It's a legitimate distinction, I think. But still one that may be reproducible in a lab.

That is the point I was trying to make. I appologize, if I was not clear.

Are you saying that taking dog DNA and modifying it in one fell swoop to horse DNA would be sufficient? Or would you need to see a series of steps in between?

sentientsynth said:
Thing is, you could hop straight from a dog to a horse with, say, several tens of thousands of specific base substitutions. My question is, just how much can we tinker with existing DNA? How much can we change it? How little can we change and get away with it? Are there different cut-offs for different species?

You are getting into an area that is way beyond my expertise. I would assume that if researchers in this area were aware of "cut-offs" for different species they would tell us.

sentientsynth said:
Exciting questions, to me. But I keep reminding myself that this is the sort of thing I've always seen in those cheesy 80's science B-movies. Well, Island of Dr. Moreau was pretty good. Freaky, though. And exactly like what I'm talking about doing. Well, minus the human factor.

We should be careful not to let our science fiction dictate our science.

sentientsynth said:
Anyway, back to the subject. I wouldn't even demand that it be as big, bold, and nasty as a dog to a horse. How about one species of kingdom Archeabacteria to another within the same kingdom? Swap things that are very similar genomics-wise. Then slowly increase the species differential. How far can you go, making whatever slight modifications are necessary? Which would lead us to the final question, How slight or how large does a modification have to be for a given species, for a given phenomic modification?

I love it when people say things are impossible with science.


Then let's lower it. What you said sounded reasonable. But...just how high is the bar for evolution? That's what I want to get at. Not to find out how we got here, but if it's even possible. A pure science endeavor.


Occam's razor has its exceptions. But I'm sure you know that.


That's pretty much my point. But I'm not satisfied with an argument from ignorance. I want data. Something. Anything that answers my questions.


Well, believe that if you like. But if you were arguing the mechanism of a certain, unknown chemical reaction and you presented argumentation analogous to what you've shown here, I'd be forced to kick you off my staff. Sorry. I've been accused of mixing up the scientific method and formal logic. The charge may hold true.

Neither am I, satisfied with an argument from ignorance that is. That is why I would need to see a mechanism that would stop micro-evolution from turning into macro-evolution. As far as I can tell this idea that there is a physical limit between the scope of evolutionary change is an argument from ignorance.

Well let's just say that I am fortunate I am not on your staff.

The scientific method always uses logic. But logic does not always use the scientific method.
 

bob b

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DNA can change radically within a few generations due to the natural processes of sexual recombination and natural/artificial selection. See the news article out today about a hybrid polar bear/grizzly. Ditto for lion/tiger, dolphin/killer whale and many others.

http://www.nytimes.com/aponline/world/AP-Hybrid-Bear.html

Mutations may have been given too much credit as an agent of change in lifeforms.
 
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sentientsynth

New member
bob b said:
DNA can change radically within a few generations due to the natural processes of sexual recombination and natural/artificial selection. See the news article out today about a hybrid polar bear/grizzly. Ditto for lion/tiger, dolphin/killer whale and many others.

http://www.nytimes.com/aponline/world/AP-Hybrid-Bear.html

Mutations may have been given too much credit as an agent of change in lifeforms.

Bob,

Thanks for that link. A question though. Isn't it true that species like this won't breed in the wild? Don't they have to be put in captivity together before they'll mate this way?

Inhowfar would you think this would detract from your overall observation concerning genetic recombination?


Thanks,

SS
 

bob b

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sentientsynth said:
Bob,

Thanks for that link. A question though. Isn't it true that species like this won't breed in the wild? Don't they have to be put in captivity together before they'll mate this way?

SS

The recent episode of the shooting of a polar bear/grizzley in the wild seems to work against your thesis.

The truth is that no evolutionist likes to consider the effects of cross breeding in the wild, probably because this might detract from the favored mutation/natural selection scenario.

aharvey once accused me of being silly to suggest that all species could have descended from a few original "types" in only the 6000 odd years since creation, because that would be "hyperevolution". This despite the abundant evidence that this a far more realistic scenario than the mutation/natural selection/"over millions of years from a primitive protocell" scenario.
 

Johnny

New member
bob b said:
The truth is that no evolutionist likes to consider the effects of cross breeding in the wild, probably because this might detract from the favored mutation/natural selection scenario.
Had you actually ever spent time in a college-level biology classroom, you might not have such wildly wrong and misinformed opinions. Further, if you'd actually take the time to study the subject in any capacity, you might also prevent yourself from looking like the dunce you do now. The effects of cross breeding have been studied as long as you've been alive. I spent a good deal of time studying them in general biology 2. Yes, that's a freshman course. I don't appreciate you traipsing in here and just spouting off about something with little regard for the truth. You're wrong--it has been discussed and studied at length as long as the discipline has been around.

From the year 1932, "The roles of mutation, inbreeding, crossbreeding and selection in evolution"
aharvey once accused me of being silly to suggest that all species could have descended from a few original "types" in only the 6000 odd years since creation, because that would be "hyperevolution".
The silliness of your claim can be demonstrated quite simply. Not even you believe it--because uphill mutations don't happen. And even though a polar bear and a grizzly bear can interbreed, there is quite a lot of difference between them. If they came from the same kind, one or both of them would have had to have gone uphill in some way or another. But alas, all mutations are downhill, and interspecific breeding yields no new genetic information. You're up a river either way, but I'd like to see which concession you'll make first. So, a few "kinds" with hyper-evolution of new information, or lots of kinds with no new information?
 

Yorzhik

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Johnny said:
Before we continue, can you summarize your understanding of cellular replication, DNA reproduction, and DNA transcription and translation? Just a short paragraph will suffice. Rereading one of your older posts I kind of felt like you were missing something. You said, "The odds are against the idea that a pure strain will survive generation through generation, stacking good mutation upon good mutation in their DNA."
Here is how you seem to be saying this works: Take a population, and within this population there is an individual that gets a very good mutation. The rest of the population will either have no mutations, bad mutations, neutral mutations, or good mutations that are not as good as the very good mutation. The individual's genes with the best mutation will be spread through the population and after being fixed in the population another very good mutation will come along and spread through the population. Also, along the way, those individuals with bad mutations are removed from the population. If this is a correct overview of how evo works, then what we will have is an individual organism whose ancestry avoided bad mutations, and is the product of many good mutations - a pure strain.

Yorzhik said:
Both are still undirected changes that when added up (despite some like these) tend to break down the DNA.
Johnny said:
How? You haven't explained this.
That would be the definition of mutations, wouldn't it?

Johnny said:
Can you give me an example of a "new system" that would be required to make one body type into another body type?
For instance, the ancestors of mammals didn't have mammary glands. And this is just one of the obvious examples. But the real problem lies in the plethora of interconnected systems that make it and integrate it into the body.

A simple way to recognize this is that the first common ancestor could not possibly have had all the systems of all the organisms that exist today. Something had to be new somewhere along the line.

Johnny said:
No, it does matter. You said, "Because not only will a good mutation have to be changed in whatever point it did change, but it will have to also come with changes (or wait for changes) to other systems that are dependent on that other single change." I provided a mechanism by which a mutation would not have to come with changes or wait for changes in other systems dependent on that single change.
You gave a mechanism? No, you gave an example. This would be like someone watching the craps table and seeing the house win in Las Vegas. After a while they ask how to win at craps... i.e. they are looking for that mechanism that would allow them to beat the house - and you respond with someone who won a bet at the table!

But it gets worse in that the probabilities of winning at craps are vastly better than mutations giving you new integrated systems in your DNA.

Johnny said:
It appears you're defining any change away from the "starting" genotype as a "breakdown". In that case, I can breakdown all the way from a monkey to a man and your definition of breakdown (whatever it may be) becomes meaningless.
No. I mean that the changes will break things in the DNA so the organism eventually can no long function.

Johnny said:
No, I don't think you understood what I was saying. You can't classify multiple copies as redundant or primary--they are functional equivalents. It's like having four copy machines in a room that do the same thing, and each time you need one you pick one randomly. You can't classify one as a primary machine and the rest as secondary or tertiary backups--they are all primary machines. If you knock out one, you haven't lost the ability to make copies. Which means that your clients who rely on that copy still get their papers.
First, I didn't say "primary and secondary", I said "redundant" - which is what you are describing here.

Second, my point was that the extra copies aren't always redundant.

Johnny said:
Mutations are either good or bad. The bad ones get eliminated, the good ones live on. Thus, bad mutations are just as important for natural selection as good mutations.
Yes, but not every bad mutation gets weeded out of the population. In fact, mutational load is a big consideration in genetics. If "The bad ones get eliminated", then mutational load would not be significant.

Yorzhik said:
It's absurd to believe that mutations, even some good ones, prove that evolution from protocell to human cell occurred?
And the rest of the quote after that question:
Yorzhik said:
That isn't absurd. I'm only going as far as the science allows. You are going from "see, mutations exist and we can imagine a protocell" to "humans exist therefore evolution went from protocell to human". It's just proving evolution because we are here.
Johnny said:
Mutations do not prove evolution from a protocell, they provide a mechanism.
I apologize, my quote was not clear. I guess now is a good time to repeat that when using the word "prove" in these kinds of discussions means "provide strong evidence for". I'll provide the same courtesy to you.

Thus, if we can get mutations to change one body type into another body type without direction in the lab that would be strong evidence that evo is true.

But I'm glad you're admitting that mutations provide the mechanism. Let's see if we can test that theory and find out just what mutations can do and how well they work to change a protocell into a human.

yorzhik said:
You are going from "see, mutations exist and we can imagine a protocell" to "humans exist therefore evolution went from protocell to human". It's just proving evolution because we are here.
Johnny said:
I am directly telling you right now that I am making no such assertion. The assertion I was trying to make was that it's absurd to speculate over the impossibility of a good mutation happening when it happens all the time.
I'm not speculating over the possibility of a good mutation happening. I agree they happen. Your assertion is that good mutations happen, so that somehow lends weight to evo's claim that a protocell, via good mutations, can turn into a human. And do they actually look at how mutations affect the DNA? That isn't checked into too much because it obviously couldn't possibly be the case. And so what evidence is given that mutations can do what evo claims? Do you know if any other evidence provided other than "we are here"? What evidence is that?

Johnny said:
Einstein's theory.

Einstein's theory.



Quantum theory is probably the only viable competitor at the moment; but there is no empirical support for the graviton.
Yes, thank you. What needs to be pointed out is that there is more than one theory of gravity, and we really don't know which one is right. We also cannot say that some of the more speculative theories of gravity are wrong. We also cannot say that evolution is an observable phenomenon like gravity is, but is a theory that attempts to explain the observable phenomenon of living things.

Johnny said:
When a creationist says evolution is only a theory, what he's really saying (much to his dismay) is "evolution is a logically self-consistent description of natural phenomena which is supported by experimental evidence and is predictive, logical, and testable." Wikipedia says, "A [scientific] theory is a logically self-consistent model or framework for describing the behavior of a related set of natural or social phenomena. It originates from and/or is supported by experimental evidence (see scientific method). In this sense, a theory is a systematic and formalized expression of all previous observations that is predictive, logical and testable. In principle, scientific theories are always tentative, and subject to corrections or inclusion in a yet wider theory."
If the assumptions that evo claims are true, then it is internally consistent. The problem is that the assumptions evo makes are wrong in spectacular ways.
 

Johnny

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For instance, the ancestors of mammals didn't have mammary glands. And this is just one of the obvious examples. But the real problem lies in the plethora of interconnected systems that make it and integrate it into the body.
Like what? Be specific.
A simple way to recognize this is that the first common ancestor could not possibly have had all the systems of all the organisms that exist today. Something had to be new somewhere along the line.
Of course.
You gave a mechanism? No, you gave an example.
What are you talking about? Mechanism: "An instrument or a process, physical or mental, by which something is done or comes into being" (dictionary.com) You said, "Because not only will a good mutation have to be changed in whatever point it did change, but it will have to also come with changes (or wait for changes) to other systems that are dependent on that other single change." I provided an instrument or process...by which a mutation could occur without having to wait on changes in other systems. That is, by definition, a mechanism. This is not a difficult concept.

This would be like someone watching the craps table and seeing the house win in Las Vegas. After a while they ask how to win at craps... i.e. they are looking for that mechanism that would allow them to beat the house - and you respond with someone who won a bet at the table!
That is in no way analogous.
Second, my point was that the extra copies aren't always redundant.
Not always, so what? What if a bacteria which once relied on higher expression levels of a protein no longer needs elevated expression. The extra copies are now redundant--and their mutation and subsequent selection will have no effect on systems dependent upon the protein.
Thus, if we can get mutations to change one body type into another body type without direction in the lab that would be strong evidence that evo is true.
No, it would be strong evidence in the lab as well.
And do they actually look at how mutations affect the DNA? That isn't checked into too much because it obviously couldn't possibly be the case.
Yes, they do.
Yes, thank you. What needs to be pointed out is that there is more than one theory of gravity, and we really don't know which one is right.
No, there is only one theory of gravity supported by mounds of empirical evidence. The other "theory" of gravity is a paper theory which exists soley to reconcile an apparent conflict. It is not a "theory" in the classical sense.

Edited a large chunk of this out. It wasn't really appropriate.
 
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Yorzhik

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Yorzhik said:
For instance, the ancestors of mammals didn't have mammary glands. And this is just one of the obvious examples. But the real problem lies in the plethora of interconnected systems that make it and integrate it into the body.
Johnny said:
Like what? Be specific.
Sticking with the example of mammary glands, there are signals from a fertilized egg that prompt changes to begin so the glands can function differently from when lactation is not required. This signal is not the change itself, but the signal must be generated and interpreted and transmitted outside of the gland. And that is just one example, but it should be enough.

Yorzhik said:
A simple way to recognize this is that the first common ancestor could not possibly have had all the systems of all the organisms that exist today. Something had to be new somewhere along the line.
Johnny said:
Of course.
But the new systems could not have been created from mutations. There are to many interconnected systems. Or another way to put it; the feedback control mechanisms inside the organisms would too quickly get confused (break) if mutations were allowed to change the signals beyond a certain range.

Johnny said:
What are you talking about? Mechanism: "An instrument or a process, physical or mental, by which something is done or comes into being" (dictionary.com) You said, "Because not only will a good mutation have to be changed in whatever point it did change, but it will have to also come with changes (or wait for changes) to other systems that are dependent on that other single change." I provided an instrument or process...by which a mutation could occur without having to wait on changes in other systems. That is, by definition, a mechanism. This is not a difficult concept.
Even though I think you understood what I meant, I'm sure you won't admit it. So let me be clearer; Mutations can change things, but sometimes a system requires more than one change to disparate parts to function. In fact, if you are creating new organs, then that would be the norm. So, the instrument or process you provided was a mutation that created a cascade of changes, but that is not a mechanism to create changes necessary in other systems that need to take place for the system with that single change to function.

Yorzhik said:
This would be like someone watching the craps table and seeing the house win in Las Vegas. After a while they ask how to win at craps... i.e. they are looking for that mechanism that would allow them to beat the house - and you respond with someone who won a bet at the table!
Johnny said:
That is in no way analogous.
No, this is very analogous. I can see why OEJ was getting frustrated with you.

How would you beat the house at craps? Always roll a winning number (or more accurately, predict what number will be rolled with a sufficiently high enough degree of accuracy), but if you can always roll what you want, prediction is intrinsic.

Money is analogous to functions in the organism. The house winning is analogous to death. You breaking even is analogous to staying a particular species (not gaining functions that increase fitness, but not losing any either). And winning is analogous to gaining function that help increase fitness. And the linchpin to this analogy: Rolling dice is analogous to random mutation. And even more apropos to the analogy, you cannot just guess what you are going to roll, but make sure you get a roll that will work - i.e. not all functions that become available from a mutation/roll will give you better fitness. In fact, most won't.

So now, if you can tell us how we can roll what we want in the game of craps, then we could insure that we would win. And the operative word is "how" i.e. the mechanism. This is what I've been asking all along. And I have been clear that I'm not asking for an example of a winning roll, but that I'm asking how you beat the house. I'm contending that you are claiming that an example of a winning roll is what you say the mechanism is, a single mutation.

All analogies break down at some point, but this one keeps going at least a little further. I ask you: what are your chances of beating the house (assuming you cannot roll what you want when you want) if you stay at the table and play for 5 billion years, greater or worse?

Yorzhik said:
Second, my point was that the extra copies aren't always redundant.
Johnny said:
Not always, so what? What if a bacteria which once relied on higher expression levels of a protein no longer needs elevated expression. The extra copies are now redundant--and their mutation and subsequent selection will have no effect on systems dependent upon the protein.
"What if it worked out just so if it were redundant or not, that way just happened to be better for the organism!" Well, gee, I guess then it always would be better.

It doesn't matter (in the real world). In the real world even if you did sometimes get it right, those times that you don't will contribute, at best, to mutational load.

Yorzhik said:
Thus, if we can get mutations to change one body type into another body type without direction in the lab that would be strong evidence that evo is true.
Johnny said:
No, it would be strong evidence in the lab as well.
Sorry, a more clear way to have said that would have been "even in the lab". I realize that if you can duplicate conditions in the lab it would be a valid test. The point was that (even if it were a lab test), turning one body type into another via mutation would have to be done with undirected mutations. If you can do that, then you've got about a slam dunk that evolution is true.

But let's go another step back, even if you could get a good mutation (a long way from changing one body type into another body type) that would be evidence that evolution was true, too. However, despite a step in the right direction, you have to take your organism with the good mutation and continue to subject it to mutations until you get another good one. Every good mutation is another step toward "proving" evolution. And BTW, no rewinding.

Yorzhik said:
And do they actually look at how mutations affect the DNA? That isn't checked into too much because it obviously couldn't possibly be the case.
Johnny said:
Yes, they do.
No they don't. And I'll make a prediction that if they ever did tell us, it would be obvious to the most casual observer that evolution has no way to turn one body type into another body type, that mutational load would kill any organism that mutated enough to do it.

Or perhaps they do it and they won't tell anyone. Have you ever tried to get a straight answer on a measure of a particular specie's mutational load?

Yorzhik said:
Yes, thank you. What needs to be pointed out is that there is more than one theory of gravity, and we really don't know which one is right.
Johnny said:
No, there is only one theory of gravity supported by mounds of empirical evidence. The other "theory" of gravity is a paper theory which exists soley to reconcile an apparent conflict. It is not a "theory" in the classical sense.
So we can ignore the theory that's on paper, right? Since it isn't a "theory in the classical sense" (if you can easily define "theory in the classical sense" that would help greatly) it cannot possibly be correct. Please note; these two theories happen to be exclusive to each other - they cannot both be completely correct at the same time.
 
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