[_ Old Earth _] The Amazing Discovery of DNA

[jasoncran]

Certainly there is that possibility, but I was addressing the assertion that the majority of the community thinks in a certain way. Also, the OP said "Crick concluded...." which seems like a powerful statement until you think about the fact that a) he conducted the majority of his research 50 years ago, and b) he is dead. (Also, C) he was an ardent opponent of creationism)

Personally, I fail to see how someone could look at the unbelievable complexity of life and seek to explain it without evolution. As Dobzhansky famously said: "Nothing in biology makes sense except in the light of evolution".

People do not give up their views easily, and almost never when confronted with an opposing view from another individual. New views are generally only acquired through personal experience and through force-feeding. I certainly don't think I will change any minds with my posts.

What is important to me is the truth. I have no problem with someone having a personal belief, but take issue when they start espousing utter nonsense that is flat out wrong (eg. the majority of the scientific community believes in a designer). This gives someone attempting to make their own decision a false impression of the issue.

And jason, I know it has been pointed out numerous times that current Evolutionary Biology has moved FAR beyond Darwin. Darwin never even read Mendel's work, so their clearly were some gaping holes in his theory - but the general concepts have provided a framework from which to expand upon.

i know that but that isnt even said anymore, how can it gradual still? when the fossils and the dna cant be verified. macro isnt observable via dna if said species is just a tad different.we cant observe to see if a populous wasnt there and had been there indenpendelety from each other, and see my post on dna mutations isssue that kinda stymies that.

 

[abrown9]

i know that but that isnt even said anymore, how can it gradual still? when the fossils and the dna cant be verified. macro isnt observable via dna if said species is just a tad different.we cant observe to see if a populous wasnt there and had been there indenpendelety from each other, and see my post on dna mutations isssue that kinda stymies that.

I'm a little confused by your argument (and also am new to the thread), so if possible, could you present your arguments piecemeal in a new post? Thanks.

As for the gradualism - I'm personally a advocate of Gould's punctuated equilibrium (or at least a mixture of PE and gradualism). Mutation rates (in my opinion) are not constant and that makes the molecular clock very flawed.

 

[jasoncran]

I'm a little confused by your argument (and also am new to the thread), so if possible, could you present your arguments piecemeal in a new post? Thanks.

As for the gradualism - I'm personally a advocate of Gould's punctuated equilibrium (or at least a mixture of PE and gradualism). Mutation rates (in my opinion) are not constant and that makes the molecular clock very flawed.

that isnt whats taught btw and neither could that be explained sudden evolution speed up and slows down.! theres a ton of insect of non hominid fossils to look for as proof. care to pick a species that has ton of verifable itermidiates. and here

 

[jasoncran]

this can you answer how this doesnt hurt macroevolution. how many of these links are needed to change from one species or rather kingdom to another?

if more then seven it didnt happen and aint gonna per this article

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

 

[abrown9]

Well, I must confess that I don't really remember what I was taught in highschool. I certainly was taught PE in University. I could see gradualism being taught in the same manner as the Bohr Model is taught. Not completely correct, but gets some general ideas across for students to comprehend. That being said, I'm not a huge fan of teaching the Bohr model.

As for your article, the author makes the mistake in calculating the probability that the one enzyme will co-opt to the function of the new enzyme (requiring 7 changes). The timeframe needed for these exact 7 changes to occur (accounting for the randomness of mutation) would need to be longer than the earth has existed (note that the author cites THEIR OWN PAPER FROM THE SAME JOURNAL for this little factoid...just an aside).

The real problem is that this line of reasoning falls into a "sharpshooter" fallacy, where the author is attempting to calculate the probability of 7 precise changes occurring. There are many, many possibilities for other functional homologs that didn't occur, but could have if different changes had happen. In the sharpshooter fallacy, the problem lies in ignoring the other possibilities. By saying the odds of X occurring are 1 in whatever billion, the author is implying that X is the only possible result.

A good analogy is a deck of cards. If someone throws down a deck of cards and randomly picks them up, the odds of a certain order coming up are ridiculously high. There are, however, many other possibilities that are equally unlikely. One of them has to happen.

Seven random mutations leading to any new co-opt isn't that unlikely. Certainly 7 unique mutations leading to that SPECIFIC co-opt are very unlikely, but by only testing that one conversion of function, the authors are ignoring all other possibilities. The evolution of life is not predestined. We are only observing the result of one of many, many possibilities.

As a sidenote, the Biologic Institute is funded by an organization whose main goal is to prove intelligent design through science.

 

[jasoncran]

Well, I must confess that I don't really remember what I was taught in highschool. I certainly was taught PE in University. I could see gradualism being taught in the same manner as the Bohr Model is taught. Not completely correct, but gets some general ideas across for students to comprehend. That being said, I'm not a huge fan of teaching the Bohr model.

As for your article, the author makes the mistake in calculating the probability that the one enzyme will co-opt to the function of the new enzyme (requiring 7 changes). The timeframe needed for these exact 7 changes to occur (accounting for the randomness of mutation) would need to be longer than the earth has existed (note that the author cites THEIR OWN PAPER FROM THE SAME JOURNAL for this little factoid...just an aside).

The real problem is that this line of reasoning falls into a "sharpshooter" fallacy, where the author is attempting to calculate the probability of 7 precise changes occurring. There are many, many possibilities for other functional homologs that didn't occur, but could have if different changes had happen. In the sharpshooter fallacy, the problem lies in ignoring the other possibilities. By saying the odds of X occurring are 1 in whatever billion, the author is implying that X is the only possible result.

A good analogy is a deck of cards. If someone throws down a deck of cards and randomly picks them up, the odds of a certain order coming up are ridiculously high. There are, however, many other possibilities that are equally unlikely. One of them has to happen.

Seven random mutations leading to any new co-opt isn't that unlikely. Certainly 7 unique mutations leading to that SPECIFIC co-opt are very unlikely, but by only testing that one conversion of function, the authors are ignoring all other possibilities. The evolution of life is not predestined. We are only observing the result of one of many, many possibilities.

As a sidenote, the Biologic Institute is funded by an organization whose main goal is to prove intelligent design through science.

biologos you mean

 

[abrown9]

biologos you mean

The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway
Ann K. Gauger and Douglas D. Axe*
Biologic Institute, Redmond, WA, USA

Maybe the page I found it on had it wrong. Regardless, does that answer suffice?

 

[jasoncran]

The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway
Ann K. Gauger and Douglas D. Axe*
Biologic Institute, Redmond, WA, USA

Maybe the page I found it on had it wrong. Regardless, does that answer suffice?

i heard that one but that is the case study i posted.let me ask you this, how many and how rapidly would the cambrain have to be and how many nucleotides changes,. remember if one little change is occured then no-go and the fossils are there to show that. only fully formed are there. i dont think we go from the early hagfish and its predecessor without some gradual changes.

lamprays to the following fish that vertibrates. what massive or minor changes would have with occur for them to have jaws and teeth? and explosive in nature. hagfish were around since the denovian but you claim and explosion so where is it in the dna and how much change would have to occur for a spine to grow and add the other things fish has?

 

[abrown9]

i heard that one but that is the case study i posted.let me ask you this, how many and how rapidly would the cambrain have to be and how many nucleotides changes,. remember if one little change is occured then no-go and the fossils are there to show that. only fully formed are there. i dont think we go from the early hagfish and its predecessor without some gradual changes.

lamprays to the following fish that vertibrates. what massive or minor changes would have with occur for them to have jaws and teeth? and explosive in nature. hagfish were around since the denovian but you claim and explosion so where is it in the dna and how much change would have to occur for a spine to grow and add the other things fish has?

Jason, I'm not going to get into a debate about the Cambrian explosion based on some broad, sweeping, inflammatory statements. Your question seems to be "too much change occurred for it to be possible to occur, explain". You provided a specific question to which I provided a specific response. You subsequently ignored that response and posed an extremely broad question that I can't possibly hope to answer short of writing a book. If you have a response to my post or another specific question, I'd be happy to discuss it with you.

I suggest you read "Is the Cambrian Explosion a Sigmund Fraud?", by Stephen Gould. Our fossil records from the Cambrian show numerous (many more than currently exist) lines of species that went extinct shortly after their radiation. This implies a massive environmental change that led to massive adaptation in some very bizarre ways. Gould provides some excellent insight into what that environmental change could possibly be.

It seems to me that a creator wouldn't just roll the dice and hope for the best (which is exactly what happened in the Cambrian).

 

[jasoncran]

Jason, I'm not going to get into a debate about the Cambrian explosion based on some broad, sweeping, inflammatory statements. Your question seems to be "too much change occurred for it to be possible to occur, explain". You provided a specific question to which I provided a specific response. You subsequently ignored that response and posed an extremely broad question that I can't possibly hope to answer short of writing a book. If you have a response to my post or another specific question, I'd be happy to discuss it with you.

I suggest you read "Is the Cambrian Explosion a Sigmund Fraud?", by Stephen Gould. Our fossil records from the Cambrian show numerous (many more than currently exist) lines of species that went extinct shortly after their radiation. This implies a massive environmental change that led to massive adaptation in some very bizarre ways. Gould provides some excellent insight into what that environmental change could possibly be.

It seems to me that a creator wouldn't just roll the dice and hope for the best (which is exactly what happened in the Cambrian).

possibly be eh. why not is that science, you could have named one species i even listed where to start.

pick one species, inflammatory? eh ? where did i attack you. you claimed seven nucleotide sequences are rare and i asked how much info was gained or lost when the cambrian explosion. so species just popped in? we could start with the earliest fish or any fish.

you pick. i followed you thinking, i asked if such diversity is found in life in that era then how much changes were to occur in the kindgoms.


ignored? no i had a response but i had choosen a wrong species.

to go from non-vertabrate and to vertabrate is a big step is it not. surely it has to be less then seven nucleotides.
that is why i mentioned hag fish as in my google i had found they were there in that era. roll the dice eh. now God didnt roll the dice, buddy.
so i should ignore dna evidence then and also fossil as its thrown out since we dont have evidence for the early vertabrates?

what isnt specific on this, i ask where did the first jawed fish come from in that era that evolved from hagfish and wheres the dna to show the change. is that specific now?

lamprays to the following fish that vertibrates. what massive or minor changes would have with occur for them to have jaws and teeth? and explosive in nature. hagfish were around since the denovian but you claim and explosion so where is it in the dna and how much change would have to occur for a spine to grow and add the other things fish has?

 

[abrown9]

possibly be eh. why not is that science, you could have named one species i even listed where to start.

pick one species, inflammatory? eh ? where did i attack you. you claimed seven nucleotide sequences are rare and i asked how much info was gained or lost when the cambrian explosion. so species just popped in? we could start with the earliest fish or any fish.

you pick. i followed you thinking, i asked if such diversity is found in life in that era then how much changes were to occur in the kindgoms.


ignored? no i had a response but i had choosen a wrong species.

to go from non-vertabrate and to vertabrate is a big step is it not. surely it has to be less then seven nucleotides.
that is why i mentioned hag fish as in my google i had found they were there in that era. roll the dice eh. now God didnt roll the dice, buddy.
so i should ignore dna evidence then and also fossil as its thrown out since we dont have evidence for the early vertabrates?

what isnt specific on this, i ask where did the first jawed fish come from in that era that evolved from hagfish and wheres the dna to show the change. is that specific now?

Okay, first, you asked a question about one enzyme co-opting to serve another function (which is specific), and then jumped WAY back to the radiation of all life. Your question about lamprey to gnathostome development is also very broad.

To properly understand how such changes happen, one has to understand epigenetics. Epigenetics (epi = above) is exactly how it sounds = above genetics. These are changes dealing with transcription factors (among other things such as RNAi and the histone code) - simple proteins that are involved heavily in gene regulation. Its a lot more complicated than X amount of nucleotides changed and the result is Y structure.

One transcription factor can regulate the expression of entire limbs, so small functional changes in TFs from one generation to the next can mean MASSIVE morphological changes. I'm far from an expert, so I can't give you a great explanation of how TF evolution parallels vertebrate evolution, but I do know there are ortholog TFs between lampreys and what are considered "primitive" gnathostomes (www.pnas.org/content/98/4/1665.short).

 

[jasoncran]

link doesnt work , if its short post it here as i try to do with a copy of the link to show that you or i didnt steal it.

 

[abrown9]

Yea, this forum is really odd with links. Here is the abstract.

Lamprey Dlx genes and early vertebrate evolution
Adam H. Neidert, Vikrant Virupannavar, Gillian W. Hooker, and James A. Langeland*

Gnathostome vertebrates have multiple members of the Dlx family of transcription factors that are expressed during the development of several tissues considered to be vertebrate synapomorphies, including the forebrain, cranial neural crest, placodes, and pharyngeal arches. The Dlx gene family thus presents an ideal system in which to examine the relationship between gene duplication and morphological innovation during vertebrate evolution. Toward this end, we have cloned Dlx genes from the lamprey Petromyzon marinus, an agnathan vertebrate that occupies a critical phylogenetic position between cephalochordates and gnathostomes. We have identified four Dlx genes in P. marinus, whose orthology with gnathostome Dlx genes provides a model for how this gene family evolved in the vertebrate lineage. Differential expression of these lamprey Dlx genes in the forebrain, cranial neural crest, pharyngeal arches, and sensory placodes of lamprey embryos provides insight into the developmental evolution of these structures as well as a model of regulatory evolution after Dlx gene duplication events.

 

[jasoncran]

i understand that is gradual but how in the word does one say now its not? if its rapid then it must be fast and have casualities as its rapid, of course rapid isnt problably as fast as i think but not a gradual as before. i will wait to see you post on that link issue.

 

[abrown9]

i understand that is gradual but how in the word does one say now its not? if its rapid then it must be fast and have casualities as its rapid, of course rapid isnt problably as fast as i think but not a gradual as before. i will wait to see you post on that link issue.

I don't really understand what you're trying to get at here. The C explosion certainly was rapid by evolutionary standpoints (although still over many, many millennia). Life radiated explosively and has stayed fairly constant since then (with only further adaptations on the original groupings that emerged in the Cambrian explosion). An interesting explanation that I have heard is the idea that the Earth has a carrying capacity for variation. When things grow (such as the growth of diversity) in a system with an upper limit for carrying capacity, then their growth patter exhibits a sigmoidal curve. The pre-cambrian dearth of diversity is considered the initial slow increase, the explosion is considered the log or exponential phase, and the period onwards until now is considered the stationary phase. Its very similar to bacterial populations growing in a media.

 

[jasoncran]

I don't really understand what you're trying to get at here. The C explosion certainly was rapid by evolutionary standpoints (although still over many, many millennia). Life radiated explosively and has stayed fairly constant since then (with only further adaptations on the original groupings that emerged in the Cambrian explosion). An interesting explanation that I have heard is the idea that the Earth has a carrying capacity for variation. When things grow (such as the growth of diversity) in a system with an upper limit for carrying capacity, then their growth patter exhibits a sigmoidal curve. The pre-cambrian dearth of diversity is considered the initial slow increase, the explosion is considered the log or exponential phase, and the period onwards until now is considered the stationary phase. Its very similar to bacterial populations growing in a media.

can you fix the link? or post it here.
not all scientist buy that phase from what i read.and that speed of level of explosion is what i read.

i hate to be broad but in as best as possible what is accounted for the sudden return to normal slow gradual change and also what somewhat drove the speed up isnt really answered as the enviroment must select the genes not speed them up in mutation rates(this is what cornfuses me on that).

 

[jasoncran]

ok, i didnt see that link posted sorry.

 

[abrown9]

can you fix the link? or post it here.
not all scientist buy that phase from what i read.and that speed of level of explosion is what i read.

i hate to be broad but in as best as possible what is accounted for the sudden return to normal slow gradual change and also what somewhat drove the speed up isnt really answered as the enviroment must select the genes not speed them up in mutation rates(this is what cornfuses me on that).

Ah okay, I think I understand your question now. An interesting explanation I've heard for changes in mutation rates is the transposon explanation (this is from a chapter of Survival of the Sickest, by Sharon Moalem, an excellent read with fairly simple prose). Transposons or "jumping genes" are transposable elements that insert themselves "randomly" throughout the genome. Transposons were long considered to be completely random and not directed. It appears that in times of stress (such as rapid environmental change), transposons will insert preferentially (thus mutating) into a region of the genome that tends to produce significant phenotypic changes when mutated. This might indicate a pretty big evolutionary role and also explain changes in mutation rates over time.

 

[jasoncran]

Ah okay, I think I understand your question now. An interesting explanation I've heard for changes in mutation rates is the transposon explanation (this is from a chapter of Survival of the Sickest, by Sharon Moalem, an excellent read with fairly simple prose). Transposons or "jumping genes" are transposable elements that insert themselves "randomly" throughout the genome. Transposons were long considered to be completely random and not directed. It appears that in times of stress (such as rapid environmental change), transposons will insert preferentially (thus mutating) into a region of the genome that tends to produce significant phenotypic changes when mutated. This might indicate a pretty big evolutionary role and also explain changes in mutation rates over time.

i was reading up on that, i found something on that that denies that statement , its been a long day. i will google that post.

 

[Asyncritus]

Certainly there is that possibility, but I was addressing the assertion that the majority of the community thinks in a certain way.

I think you said the majority of the community thinks in a certain way.

I want to make it clear that 'the majority of the scientific community' has been wrong, will be wrong again, and is certainly wrong on this matter now.

The majority of the scientific community consists of people who have no knowledge of biology whatsoever, but are brow-beaten by the 'majority of the scientific community' which you mention!!!

So to use 'the majority of the scientific community' as support for a useless theory is a. mistaken b. misleading and c. asserting that there is support where in fact that support is merely crowd-following to the drum beat of the media and the pressures of excommunication from the said 'scientific community'.

Also, the OP said "Crick concluded...." which seems like a powerful statement until you think about the fact that a) he conducted the majority of his research 50 years ago, and b) he is dead. (Also, C) he was an ardent opponent of creationism)

It is astonishing that such a brilliant mind did not have the perspicacity to see that his and Watson's discovery of the structure of DNA was the finish of any theory of the chance production of any such molecule.

When I first discovered how the molecule was made up, I was left gasping at the ingenuity displayed, and the impossibility that it could have been other than the product of some incredible genius of a mind. Watson and Crick got nobels for their discovery. What should evolution receive for inventing such a thing, do you think?

Personally, I fail to see how someone could look at the unbelievable complexity of life and seek to explain it without evolution. As Dobzhansky famously said: "Nothing in biology makes sense except in the light of evolution".

If Dobzhansky said any such thing, then he was a bigger fool than I thought. He was a geneticist, and should have known better, as indeed, you should.

People do not give up their views easily, and almost never when confronted with an opposing view from another individual. New views are generally only acquired through personal experience and through force-feeding. I certainly don't think I will change any minds with my posts.

How else do you think the theory of evolution has gained such a foothold?

What is important to me is the truth. I have no problem with someone having a personal belief, but take issue when they start espousing utter nonsense that is flat out wrong (eg. the majority of the scientific community believes in a designer). This gives someone attempting to make their own decision a false impression of the issue.

I made no such assertion, and you are deeply mistaken if you think that I said so. Please re-read my post with a bit more attention.

And jason, I know it has been pointed out numerous times that current Evolutionary Biology has moved FAR beyond Darwin. Darwin never even read Mendel's work, so their clearly were some gaping holes in his theory - but the general concepts have provided a framework from which to expand upon.

I am amazed that the theory is even mentioned in respectable scientific circles.

Anyone with any real acquaintance with palaeontology and facing the improbability of mutations + natural selection producing the zillions of species in the Cambrian with the lack of time available to do so must certainly know the truth of what you said - that Biology has moved a LONG LONG WAY from Darwinism.

Yet,not very long ago, the Darwin Centennial celebrations were held, treating the man like some sort of pop star of the biological world.

Why was this?

I have pointed out, and will continue to point out, the utter impossibility of INSTINCT having evolved. It is truly the death of the theory of evolution, and it is up to you and other of its supporters, to gainsay the facts that I adduce.

I wish you well in your endeavours to do so.