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Author Topic:   Human Evolution (re: If evolved from apes, why still apes?)
skepticfaith
Member (Idle past 3072 days)
Posts: 71
From: NY, USA
Joined: 08-29-2006


Message 61 of 128 (453313)
02-01-2008 7:57 PM
Reply to: Message 59 by molbiogirl
02-01-2008 7:12 PM


Re: Congratulations to Kakip!!
quote:
And the answer is: Chimps are radically different from the common ancestor. As are we.

How do you know this? Where is the proof of this?

The reply below yours says otherwise too.

Where can I find information on evolution of Chimps?

The 1% thing became 5-7 % last time I checked - but this does not tell the whole story anyway.


This message is a reply to:
 Message 59 by molbiogirl, posted 02-01-2008 7:12 PM molbiogirl has responded

Replies to this message:
 Message 64 by molbiogirl, posted 02-01-2008 11:14 PM skepticfaith has not yet responded

  
skepticfaith
Member (Idle past 3072 days)
Posts: 71
From: NY, USA
Joined: 08-29-2006


Message 62 of 128 (453314)
02-01-2008 8:02 PM
Reply to: Message 60 by bluegenes
02-01-2008 7:39 PM


Re: Congratulations to Kakip!!
quote:
think it's plausible, yes, although if you'd said "tens of millions of years" then it would be even more likely. If a species happened to take the road of rapidly increasing intelligence immediately after our extinction, then a few million years could be enough.

How long did it take from ancestor of human and chimp to human?

quote:
The fact that ourselves and the dolphins seem to have greatly increased brain size and intelligence separately argues in favour of your suggestion happening eventually.

How would dolphins manipulate things though ?
I mean we use our hands - I can't imagine a dolphin being able to build something - what kind of adaptation will it need to make ?
This message is a reply to:
 Message 60 by bluegenes, posted 02-01-2008 7:39 PM bluegenes has responded

Replies to this message:
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bluegenes
Member
Posts: 2967
From: U.K.
Joined: 01-24-2007


Message 63 of 128 (453349)
02-01-2008 10:18 PM
Reply to: Message 62 by skepticfaith
02-01-2008 8:02 PM


Re: Congratulations to Kakip!!
How long did it take from ancestor of human and chimp to human?

All I can say is several million years, because experts keep revising it, and I've heard anything from four to eight million I think. Geneticists may be able to figure it out by mutation rates.

But remember, a lot of our intelligence had evolved before that. The things we value, like speech and our inventiveness are late, but chimps are far closer to us in intelligence than they are to lizards, for example, and mammals in general are intelligent, so if your speculative super intelligent creature evolved, it would most likely come from the mammals.

How would dolphins manipulate things though ?
I mean we use our hands - I can't imagine a dolphin being able to build something - what kind of adaptation will it need to make ?

I just mentioned dolphins because, like elephants and others, they show that intelligence increasing in mammals seems quite common, and happens along separate lines, making your speculative super being more likely. For dolphins to become toolmakers, returning to land would be the easiest way, and its easier for them than our fish ancestors, because they don't have to change their breathing system.

Tool making isn't everything. Maybe they philosophise. How do we know otherwise? Their brains are actually bigger than ours, I think, but then their bodies are as well.


This message is a reply to:
 Message 62 by skepticfaith, posted 02-01-2008 8:02 PM skepticfaith has not yet responded

Replies to this message:
 Message 68 by RAZD, posted 02-12-2008 8:03 PM bluegenes has responded

  
molbiogirl
Member
Posts: 1909
From: MO
Joined: 06-06-2007


Message 64 of 128 (453359)
02-01-2008 11:14 PM
Reply to: Message 61 by skepticfaith
02-01-2008 7:57 PM


Skeptic ain't so much of a skeptic, if you know what I mean.
The 1% thing became 5-7 % last time I checked - but this does not tell the whole story anyway.

www.news.cornell.edu/releases/Dec03/chimp.life.hrs.html

99 percent alike in genetic makeup, chimpanzees and humans might be even more similar were it not for what researchers call "lifestyle" changes in the 6 million years that separate us from a common ancestor.

You really need to keep up with the literature!

The reply below yours says otherwise too.

Sorry, charlie. Blue merely fleshed out what I said.

Where can I find information on evolution of Chimps?

www.scholar.google.com

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

Have at it, my friend.


This message is a reply to:
 Message 61 by skepticfaith, posted 02-01-2008 7:57 PM skepticfaith has not yet responded

Replies to this message:
 Message 67 by Wounded King, posted 02-12-2008 8:27 AM molbiogirl has responded

  
molbiogirl
Member
Posts: 1909
From: MO
Joined: 06-06-2007


Message 65 of 128 (453361)
02-01-2008 11:16 PM
Reply to: Message 62 by skepticfaith
02-01-2008 8:02 PM


Re: Congratulations to Kakip!!
How would dolphins manipulate things though ?
I mean we use our hands - I can't imagine a dolphin being able to build something - what kind of adaptation will it need to make ?

How perfectly anthropomorphic of you.

Yes, yes, Skeptic. Intelligence requires the use of hands with opposable thumbs. Otherwise, how would they hold books?


This message is a reply to:
 Message 62 by skepticfaith, posted 02-01-2008 8:02 PM skepticfaith has not yet responded

  
obvious Child
Member (Idle past 1466 days)
Posts: 661
Joined: 08-17-2006


Message 66 of 128 (453537)
02-02-2008 6:38 PM
Reply to: Message 49 by Crooked to what standard
02-01-2008 5:26 PM


Try again on the pollen claim

http://www.talkorigins.org/indexcc/CC/CC341.html

Older layers can be moved on top due to geological processes in the same fashion that an formerly vertical sediment layers becomes horizontal. One of the first major proofs for plate tectonics was an geological find where an layer was rotated 90 degrees and placed on top of parts of the older layer.

Animals that died violent deaths prove that animals died violent deaths. If I shoot an bird that was an violent death. It does not prove the flood occurred.

Fossils between two layers just mean that the organism was sticking out. Fluid mechanics, as referenced against your arguments before refute the flood alone.

Explain how evolution is wrong on its timescale.


This message is a reply to:
 Message 49 by Crooked to what standard, posted 02-01-2008 5:26 PM Crooked to what standard has not yet responded

  
Wounded King
Member (Idle past 1445 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 67 of 128 (455375)
02-12-2008 8:27 AM
Reply to: Message 64 by molbiogirl
02-01-2008 11:14 PM


Keeping up with the literature
You really need to keep up with the literature!

I'm sorry to say this molbiogirl but this statement make you look both arrogant and ignorant.

The fact that you have one press release which quotes someone using the 1% value hardly makes it the cutting edge of the scientific literature. The study which suggested a ~5% divergence when insertion-deletion events were incorporated (Britten, 2002)was widely publicised and as far as I know there have been no studies suggesting this is inaccurate and many supporting it and suggesting important roles for indels in human/chimp evolution (Wetterbom ,et al., 2006; Chen, et al.2007; Sakate, et al., 2007).

Looking at the paper the press release refers to (Clark, et al., 2003), they were looking at alignments of specific genes and seem to be talking specifically about nucleotide divergence in classical protein-coding genes. That can arguably support your claim that, 'Chimps differ from humans by less than 1% genetically', but only in a very limited way. It really needs some context to explain exactly what level of divergence you are talking about, 'genetically' is really too vague to encompass the many different comparative methods which have been used over the years for comparing the genes and now the genomes of humans and chimps.

SkepticFaith is closer to the mark when he says that such values don't tell the whole story. Having said that, his 5-7% is probably a better estimate when the entire genomic structure is taken into account rather than just the nucleotide sequences in orthologous genes.

TTFN,

WK


This message is a reply to:
 Message 64 by molbiogirl, posted 02-01-2008 11:14 PM molbiogirl has responded

Replies to this message:
 Message 71 by Blue Jay, posted 02-12-2008 9:20 PM Wounded King has responded
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RAZD
Member
Posts: 18241
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.0


Message 68 of 128 (455546)
02-12-2008 8:03 PM
Reply to: Message 63 by bluegenes
02-01-2008 10:18 PM


Dolphins
Tool making isn't everything. Maybe they philosophise. How do we know otherwise?

http://www.earthtrust.org/delrings.html

quote:
The young dolphin gives a quick flip of her head, and an undulating silver ring appears--as if by magic--in front of her. The ring is a solid, toroidal bubble two feet across--and yet it does not rise to the surface! It stands erect in the water like the rim of a magic mirror, or the doorway to an unseen dimension. For long seconds the dolphin regards its creation, from varying aspects and angles, with its vision and sonar. Seemingly making a judgement, the dolphin then quickly pulls a small silver donut from the larger structure, which collapses into small bubbles. She then "pushes" the donut, which stays just inches ahead of her rostrum, perhaps 20 feet over a period of up to 10 seconds. Then, stopping again, she regards the twisting ring for a last time and bites it--causing it to collapse into a thousand tiny bubbles which head--as they should--for the water's surface. After a few moments of reflection, she creates another.

Can you do that?

Enjoy.


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by our ability to understand
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This message is a reply to:
 Message 63 by bluegenes, posted 02-01-2008 10:18 PM bluegenes has responded

Replies to this message:
 Message 70 by bluegenes, posted 02-12-2008 8:31 PM RAZD has acknowledged this reply

  
Coragyps
Member
Posts: 5266
From: Snyder, Texas, USA
Joined: 11-12-2002
Member Rating: 6.1


Message 69 of 128 (455550)
02-12-2008 8:17 PM
Reply to: Message 62 by skepticfaith
02-01-2008 8:02 PM


Re: Congratulations to Kakip!!
How would dolphins manipulate things though ?

Thumbs:
http://www.theonion.com/content/node/28315


This message is a reply to:
 Message 62 by skepticfaith, posted 02-01-2008 8:02 PM skepticfaith has not yet responded

    
bluegenes
Member
Posts: 2967
From: U.K.
Joined: 01-24-2007


Message 70 of 128 (455553)
02-12-2008 8:31 PM
Reply to: Message 68 by RAZD
02-12-2008 8:03 PM


Dolphins
RAZD writes:

Can you do that?

No, but I can blow soap bubbles, and smoke rings.


This message is a reply to:
 Message 68 by RAZD, posted 02-12-2008 8:03 PM RAZD has acknowledged this reply

  
Blue Jay
Member (Idle past 48 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 71 of 128 (455558)
02-12-2008 9:20 PM
Reply to: Message 67 by Wounded King
02-12-2008 8:27 AM


Re: Keeping up with the literature
Indels don't change the overall sequence, though: they shift everything up or down the line, but conserve the sequence except at the location of insertion/deletion. So, whether the similarity is listed as 99% or 95% is largely a matter of viewpoint.

The sequences that were shifted are, in fact, still homologous (shared between chimps and humans).

In terms of gauging evolutionary relatedness, frameshifts are largely misleading, because, even though there is a difference in location, the sequence is still the same. Homology reaches farther than the 95% you give it by incorporating frameshifts. So, skepticfaith's assertion--that we've now found that we're not so close to chimpanzees because the difference is 5%--is flawed.


Signed,
Nobody Important (just Bluejay)
This message is a reply to:
 Message 67 by Wounded King, posted 02-12-2008 8:27 AM Wounded King has responded

Replies to this message:
 Message 72 by Wounded King, posted 02-13-2008 5:09 AM Blue Jay has responded

  
Wounded King
Member (Idle past 1445 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 72 of 128 (455621)
02-13-2008 5:09 AM
Reply to: Message 71 by Blue Jay
02-12-2008 9:20 PM


Re: Keeping up with the literature
Indels don't change the overall sequence, though

Sure they do, if by 'overall sequence' we mean the sequence within the genome. If you are talking about the 'overall sequence' of a gene which the indel is not occurring in then sure, they don't change it.

In terms of gauging evolutionary relatedness, frameshifts are largely misleading, because, even though there is a difference in location, the sequence is still the same.

Can you give some rationale for why small stretches of homologous sequence conservation are the best way of guaging 'evolutionary relatedness'.

If you think that only the protein coding sequence of traditional genes is important to evolution then you are well behind the curve.

Homology reaches farther than the 95% you give it by incorporating frameshifts.

This isn't just about frameshifts, you are still thinking at the gene level when we should be talking about the genome level.

If you want to say something overall about the genetic similarity of humans and chimps then why not look at the overall organisation of the genome. If you only restrict yourself to sequences from ORFs similar enough to align, as the research molbiogirl referenced did, then you are just front loading your search to give you higher similarity than might actually be the case in the genome as a whole.

So, skepticfaith's assertion--that we've now found that we're not so close to chimpanzees because the difference is 5%--is flawed.

In what way? molbiogirl said were were 1% different 'genetically', a vague term that could encompass any level of genetic organisation. Skeptic faith simply said he had heard a value for genetic divergence of 5-7%. In what way is his assertion any more flawed than molbiogirl's? They are both using the vague concept of genetic similarity but providing figures base on different specific genetic metrics.

Why should nucleotide divergence in alignable coding gene sequences be the holy grail of genetic divergence. We know that a large number of the mutations which appear to account for the differences between humans and chimps are not of this type.

Why is a single nucleotide substitution a better guage than a 2bp deletion for evolutionary distance? I can understand that indels can be more complex to dissect but discounting them for that reason is just one more way of biasing your analysis towards finding higher similarity.

Why restrict ourselves now that we have the tools for doing real full scale genome comparisons?

TTFN,

WK


This message is a reply to:
 Message 71 by Blue Jay, posted 02-12-2008 9:20 PM Blue Jay has responded

Replies to this message:
 Message 74 by Blue Jay, posted 02-13-2008 2:42 PM Wounded King has responded

    
molbiogirl
Member
Posts: 1909
From: MO
Joined: 06-06-2007


Message 73 of 128 (455645)
02-13-2008 9:36 AM
Reply to: Message 67 by Wounded King
02-12-2008 8:27 AM


Re: Keeping up with the literature
I'm sorry to say this molbiogirl but this statement make you look both arrogant and ignorant.

Oh for the love of pete.

It was a joke.

SF wouldn't look at the literature if you tied him to a chair and held his eyes open with clothespins.


This message is a reply to:
 Message 67 by Wounded King, posted 02-12-2008 8:27 AM Wounded King has not yet responded

  
Blue Jay
Member (Idle past 48 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 74 of 128 (455724)
02-13-2008 2:42 PM
Reply to: Message 72 by Wounded King
02-13-2008 5:09 AM


Re: Keeping up with the literature
Wounded King writes:

In what way? molbiogirl said were were 1% different 'genetically', a vague term that could encompass any level of genetic organisation. Skeptic faith simply said he had heard a value for genetic divergence of 5-7%. In what way is his assertion any more flawed than molbiogirl's? They are both using the vague concept of genetic similarity but providing figures base on different specific genetic metrics.

I guess I have to agree with this: the two ideas kind of delineate the outer boundaries of the argument, don't they?

Wounded King writes:

Why is a single nucleotide substitution a better guage than a 2bp deletion for evolutionary distance?

It's not: the two are equal gauges, because they both represent a single change in the genome. A view based on sequence-divergence puts the deletion as more influential, when in fact it represents no more evolutionary distance than the point-mutation.

This is a quote from the article you cited by Britten (PNAS, 2002), which is the only one I have been able to read yet:

It appears appropriate to me to consider the full length of the gaps in estimating the interspecies divergence. These stretches of DNA are actually absent from one and present in the other genome. In the past, indels have often simply been counted regardless of length and added to the base substitution count, because that is convenient for phylogenetics. (emphasis added)

It is convenient for phylogenetics, and it makes more sense when dealing with evolutionary distances. Sequence divergence only shows how different the two species are, not how long they've been separated from one another. Using deletion lengths (as Britten did) to represent how close humans are to chimpanzees would inflate their importance relative to point mutations, making it look like we diverged X+Y mya when, in fact, we diverged only X mya (X and Y >0).

In fact, Britten acknowledges this later in the paper:

More nucleotides are included in insertion/deletion events (3.4%) than base substitutions (1.4%) by much more than a factor of two. However, the number of events is small in comparison. About 1,000 indels listed in Tables 2 and 3 compared with about 10,000 base substitution events in this comparison of 779,142 nt between chimp and human. (emphasis added)

So, a big deletion is still just one deletion, and still happened at one time, even if it removed hundreds of nucleotides of base-pair homology. Deleting 54,773 base pairs in one swoop (or several swoops) is very different from changing 54,773 base pairs slowly over 54,773 separate mutation events. They would have the same end result, and so may represent the same amount of "sequence divergence," as per Britten's standards. But the first could have happened between me and my son (i.e. in 1 generation), while the second probably won't have happened in my evolutionary descendants 51 million years down the road (assuming my lineage lasts that long).

If you then compared these two genes (my son vs evolutionarily-distant descendant) using Britten's sequence-divergence strategy, you would then come to the conclusion that I am more closely related to my 51-million-years-down-the-road descendant than I am to my own son (at least at that locus). Multiple such deletions across the genome would make it even harder.

So, if you're talking just about genetic similarity (as I assume you are), then skepticfaith's estimate is probably closer. But, if you're talking about evolutionary relatedness (which is closer to the topic of this thread), skepticfaith's estimate is an inflation of the distinction between us and chimps.


Signed,
Nobody Important (just Bluejay)
This message is a reply to:
 Message 72 by Wounded King, posted 02-13-2008 5:09 AM Wounded King has responded

Replies to this message:
 Message 75 by Wounded King, posted 02-13-2008 7:36 PM Blue Jay has responded

  
Wounded King
Member (Idle past 1445 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 75 of 128 (455796)
02-13-2008 7:36 PM
Reply to: Message 74 by Blue Jay
02-13-2008 2:42 PM


Re: Keeping up with the literature
Using deletion lengths (as Britten did) to represent how close humans are to chimpanzees would inflate their importance relative to point mutations, making it look like we diverged X+Y mya when, in fact, we diverged only X mya (X and Y >0).

In terms of genetic similarity throughout the genome, which was what Britten was discussing, they are more important. I don't think Britten was ever suggesting that indel length should be used to estimate the time of divergence.

So, if you're talking just about genetic similarity (as I assume you are), then skepticfaith's estimate is probably closer. But, if you're talking about evolutionary relatedness (which is closer to the topic of this thread), skepticfaith's estimate is an inflation of the distinction between us and chimps.

I have to disagree. In terms of the topic in the immediate past molbiogirl was specifically talking about genetic similarity. In a broader sense the topic seems to me more about the genetic differences between the various primate species than about divergence times. I certainly don't see how what you are talking about is more relevant to 'evolutionary relatedness'.

I would agree that for constructing a phylogenetic tree you would probably be better of going with traditional approaches, I'm not sure if anyone has really tried using indels and other forms of copy number variation as a basis for such analyses. Building a phylogeny is not the be all and end all of evolutionary relatedness I would suggest.

What we are developing now is the ability to really identify mutations which are the basis of specific diferences between humans and our closest relatives, as well as learning more about variation within the human species.

TTFN,

WK


This message is a reply to:
 Message 74 by Blue Jay, posted 02-13-2008 2:42 PM Blue Jay has responded

Replies to this message:
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