Victory for evolution in Texas

[Phenomanul]

It doesn't matter if it took 20+ years to obtain 31,000+ generations in his lab... or if this could have happened within 5 years in the wild...

His experiment already provides the number of generations...!!!

Hence why a representative number for the span of a human generation is required...

[LnGrrrR]

It doesn't matter if it took 20+ years to obtain 31,000+ generations in his lab... or if this could have happened within 5 years in the wild...

His experiment already provides the number of generations...!!!

By "slowed down" I believe Elnono means that Lenski took great pains to eliminate outside factors which might cause mutation of genes.

[RandomGuy]

Sure... as soon as you address why you claimed my central argument [in this thread] was invalid... especially after you stated on three occasions that I never clearly stated what that was... that it was obfuscated...

Here I'll simplify it... "Macroevolution is not a proven fact. People should stop saying it is..."

I have said repeatedly that I will get to it, and I will.

(edit)

Part of proving that is going through the assumptions and criticisms you have to see if they carry any weight.

If they don't, and appear to be based on either ignorance, distortions, misapplications of established science, then it is safe to conclude it has been proven to a much greater degree than you assert.

The "tangents" as you like to call them bear directly on your case, whether you like it or not.

On a related note, the conference calls that only dimly concern me are over, and I have a project to prepare for turning in, so my time here will be very limited in the next few days.

[ElNono]

It doesn't matter if it took 20+ years to obtain 31,000+ generations in his lab... or if this could have happened within 5 years in the wild...
His experiment already provides the number of generations...!!!

By slowed down I mean the experiment removed a lot of added complexity in order to make studying easier.

The experiment has no environmental changes, and E.Coli has much fewer base pairs than humans, and thus is much less room for mutations (and selection).

You also making the incorrect assumption that a meaningful mutation couldn't have happened before 30,000 generations have gone by. Mutations are random. It's selection the mechanism by which such random hand of cards are eventually arranged in a way to accommodate the organism into it's surrounding environment.

You started complaining about dubious extrapolation, but you're doing exactly the same thing.

[ElNono]

Hence why a representative number for the span of a human generation is required...

It doesn't matter. It's not linear. That it took Lenski 30,000 generations under his controlled environment doesn't mean it takes 30,000 generations under every environment. It can take only 1 generation with the right set of mutations.

[Landon Donofag]

The terms macroevolution and microevolution are inventions of Creationists to create an artifical distinction where in reality there is none.

The process of evolution, as defined by science, works the same no matter what timescales you are looking at.

Even taking that into account, evolution including speciation can and has been observed both "in the field" and in the laboratory.

The Theory of Evolution is one of the most robust scientific theories in existance, and despite being easily falsifiable it never has been, nor has any alternative scientific hypothesis ever gained any ground.

Indeed, the Theory of Evolution (by Natural Selection) as it relates to the fact of evolution is a more robust and more complete scientific theory than the Theory of Gravity as it relates to the fact of gravity. And yet, nobody seems to have a problem with the Theory of Gravity, nor do they posit the existance of "Intelligent Falling".

[Phenomanul]

It doesn't matter. It's not linear. That it took Lenski 30,000 generations under his controlled environment doesn't mean it takes 30,000 generations under every environment. It can take only 1 generation with the right set of mutations.

That's all his experiment can say... because his experiment confirmed it... any other rate conjecture outside of what he found would be mere speculation... your 1 generational 'speciation' wish would defy some pretty tough probabilities...

Again, my statement was: "the ramifications of Lenski's experiment..."

I'm pretty busy too, but I'll contend your notion that his experiment somehow slowed down the E. coli's mutative rate simply because certain factors were controlled...

Lest you accuse me of accusing you of "dishonesty"... it's more along the lines of stating that "a glass is half empty" or stating that "a glass is half full"... are both valid statements, and both could very well be supported - but they are nevertheless diametric assessments of the same picture...

So let's see what we have:

Lenski grew marked E. coli bacteria in citrate containing (citric acid) agar solutions... but continually fed them DM25 solution... hmmm... his bacteria populations were always fed something ensuring that his cultures would continually reproduce... not a given in nature.

He knew that his batches were not equipped with the plasmid aided mechanisms to deliver the citrate to the interior of the E. coli bacteria... So after his blooms confirmed that this particular constraint was finally overcome, via natural mechanisms alone... it became pretty obvious that there was a notable change...

I should note that since his cultures were rebooted every 75 days, compe iveness for 'food' wasn't a big factor preventing the growth of his cultures [granted the Cit+ strains tend to reach population density limitations that weren't previously attained by Cit- strains]...

I'll quote this from wiki:

"As of February 2010[update], the E. coli populations have been under study for over 50,000 generations, and are thought to have undergone enough spontaneous mutations that every possible single point mutation in the E. coli genome should have occurred multiple times."

How is that considered a slow mutation rate, if the entire genome has had a chance to change every single one of it's base pairs given the ulative size of the population involved...???

and

"Of the 12 populations, 4 developed defects in their ability to repair DNA, greatly increasing the rate of additional mutations in those strains. Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that only 10 to 20 beneficial mutations achieved fixation in each population, with less than 100 total point mutations (including neutral mutations) reaching fixation in each population."

Note: Lenski's use of the word 'beneficial mutation' here is not to be confused with how we've been using it throughout this thread... he's talking about those that achieved fixation... which is another discussion altogether...

Of those mutations however, he identified two particular genes that were altered over time and that eventually allowed his cultures to utilize the citrate in his solutions...

This was the significant change that allowed his team to claim "evolution had been observed..."

FYI.... Freezing the bacteria was done only to help catalogue each generation for future studies (brilliant imo), but it shouldn't have interfered with the E. coli's ability to reproduce in it's comfy year round temperature of 37 °F (a perfect incubation temperature that each batch has had the benefit of 'growing' under)... You made it sound like the freezing process somehow slowed down their metabolism and by proxy their mutation rate...

[Phenomanul]

So, the answer is, essentially, "No I cannot really support my figure, now that you have actually read my source and called me on it".

I have the actual printed article... that online version (which is a revised edition BTW) doesn't include the accompanying graph from where I obtained the "40 million base pair" figure...

So exactly what are you callling me out on?

That I can't use a quoted value?

That you feel it is absolutely central to the exercise I introduced?

Like I said, feel free to use a value of 15 million base pair differences if you so desire... it doesn't make the results of my exercise any less telling...

but before you do consider this:

One of the downfalls of previous molecular genetic studies has been the limit at which chimpanzees and humans could be compared accurately. Scientists often would use only 30 or 40 known proteins or nucleic acid sequences, and then from those extrapolate their results for the entire genome. Today, however, we have the majority of the human genome sequences, practically all of which have been released and made public. This allows scientists to compare every single nucleotide base pair between humans and primates—something that was not possible prior to the human genome project. In January 2002, a study was published in which scientists had constructed and analyzed a first-generation human chimpanzee comparative genomic map. This study compared the alignments of 77,461 chimpanzee bacterial artificial chromosome (BAC) end sequences to human genomic sequences. Fujiyama and colleagues “detected candidate positions, including two clusters on human chromosome 21, that suggest large, nonrandom regions of differences between the two genomes” (2002, 295:131). In other words, the comparison revealed some “large” differences between the genomes of chimps and humans.

Amazingly, the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] This study compared the alignments of 77,461 chimpanzee sequences to human genomic sequences obtained from public databases. Of these, 36,940 end sequences were unable to be mapped to the human genome (295:131). Almost 15,000 of those sequences that did not match human sequences were speculated to “correspond to unsequenced human regions or are from chimpanzee regions that have diverged substantially from humans or did not match for other unknown reasons” (295:132). While the authors noted that the quality and usefulness of the map should “increasingly improve as the finishing of the human genome sequence proceeds” (295:134), the data already support what creationists have said for years—the 98-99% figure representing DNA similarity is grossly misleading, as revealed in a study carried out by Roy Britten of the California Ins ute of Technology (see Britten, 2002).

Exactly how misleading came to light in an article—“Jumbled DNA Separates Chimps and Humans”—published in the October 25, 2002 issue of Science. The first three sentences of the article, written by Elizabeth Pennisi (a staff writer for Science), represented a “that was then, this is now” type of admission of defeat. She wrote:

For almost 30 years, researchers have asserted that the DNA of humans and chimps is at least 98.5% identical. Now research reported here last week at the American Society for Human Genetics meeting suggests that the two primate genomes might not be quite as similar after all. A closer look has uncovered nips and tucks of logous sections of DNA that weren’t noticed in previous studies (298:719, emp. added).

Genomicists Kelly Frazer and David Cox of Perlegen Sciences in Mountain View, California, along with geneticists Evan Eichler and Devin Locke of Case Western University in Cleveland, Ohio, compared human and chimp DNA, and discovered a wide range of insertions and deletions (anywhere from between 200 bases to 10,000 bases). Cox commented: “The implications could be profound, because such genetic hiccups could disable entire genes, possibly explaining why our closest cousin seems so distant” (as quoted in Pennisi, 298:721).

Britten analyzed chimp and human genomes with a customized computer program. To quote Pennisi’s article:

He compared 779,000 bases of chimp DNA with the sequences of the human genome, both found in the public repository GenBank. Single-base changes accounted for 1.4% of the differences between the human and chimp genomes, and insertions and deletions accounted for an additional 3.4%, he reported in the 15 October [2002] Proceedings of the National Academy of Sciences. Locke’s and Frazer’s groups didn’t commit to any new estimates of the similarity between the species, but both agree that the previously accepted 98.5% mark is too high (298:721, emp. added).

While Locke’s and Frazer’s team was unwilling to commit to any new estimate of the similarity between chimps and humans, Britten was not. In fact, he led his article in the October 15, 2002 Proceedings of the National Academy of Sciences, “Divergence between Samples of Chimpanzee and Human DNA Sequences is 5%” (Britten, 99:13633-13635). In the abstract accompanying the article, he wrote: “The conclusion is that the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA” (99:13633, emp. added). The news service at NewScientist.com reported the event as follows:

It has long been held that we share 98.5 per cent of our genetic material with our closest relatives. That now appears to be wrong. In fact, we share less than 95 per cent of our genetic material, a three-fold increase in the variation between us and chimps.

The new value came to light when Roy Britten of the California Ins ute of Technology became su ious about the 98.5 per cent figure. Ironically, that number was originally derived from a technique that Britten himself developed decades ago at Caltech with colleague Dave Kohne. By measuring the temperature at which matching DNA of two species comes apart, you can work out how different they are.

But the technique only picks up a particular type of variation, called a single base subs ution. These occur whenever a single “letter” differs in corresponding strands of DNA from the two species.

But there are two other major types of variation that the previous analyses ignored. “Insertions” occur whenever a whole section of DNA appears in one species but not in the corresponding strand of the other. Likewise, “deletions” mean that a piece of DNA is missing from one species.

Together, they are termed “indels,” and Britten seized his chance to evaluate the true variation between the two species when stretches of chimp DNA were recently published on the internet by teams from the Baylor College of Medicine in Houston, Texas, and from the University of Oklahoma.

When Britten compared five stretches of chimp DNA with the corresponding pieces of human DNA, he found that single base subs utions accounted for a difference of 1.4 per cent, very close to the expected figure.

But he also found that the DNA of both species was littered with indels. His comparisons revealed that they add around another 4.0 per cent to the genetic differences (see Coghlan, 2002, emp. added).

It seems that, as time passes and scientific studies increase, humans appear to be less like chimps after all. In a separate study, Barbulescu and colleagues also uncovered another major difference in the genomes of primates and humans. In their article “A HERV-K Provirus in Chimpanzees, Bonobos, and Gorillas, but not Humans,” the authors wrote: “These observations provide very strong evidence that, for some fraction of the genome, chimpanzees, bonobos, and gorillas are more closely related to each other than they are to humans” (2001, 11:779, emp. added). The data from these results go squarely against what evolutionists have contended for decades—that chimpanzees are closer genetically to humans than they are to gorillas. Another study using interspecies representational difference analysis (RDA) between humans and gorillas revealed gorilla-specific DNA sequences (Toder, et al., 2001)—that is, gorillas possess sequences of DNA that are not found in humans. The authors of this study suggested that sequences found in gorillas but not humans “could represent either ancient sequences that got lost in other species, such as human and orang-utan, or, more likely, recent sequences which evolved or originated specifically in the gorilla genome” (9:431).

The differences between chimpanzees and humans are not limited to genomic variances. In 1998, a structural difference between the cell surfaces of humans and apes was detected. After studying tissues and blood samples from the great apes, and sixty humans from various ethnic groups, Muchmore and colleagues discovered that human cells are missing a particular form of sialic acid (a type of sugar) found in all other mammals (1998, 107[2]:187). This sialic acid molecule is found on the surface of every cell in the body, and is thought to carry out multiple cellular tasks. This seemingly “miniscule” difference can have far-reaching effects, and might explain why surgeons were unable to transplant chimp organs into humans in the 1960s. With this in mind, we never should declare, with a simple wave of the hand, “chimps are almost identical to us” simply because of a large genetic overlap.

I know you would hate the thought of having to read that article directly from a (gasp!) apologetics website... but I would caution that before you dismiss it consider that most of the quoted researchers in the excerpt above are in fact neoDarwinian Evolutionists... not Creationists...

Moving on:
Your original comparison was comparing "beneficial mutations", yet you used a specific, unsupportable number of "base pairs".

Do mutations only ever affect one base pair at at time?

LOL @ my use of the '40 million base pairs' figure being interpreted by you as being a "specific" "fact"...

Had I said, say "40,123,456" <--- Now that is a specific number...

Anyways, I didn't jump to conclusions, you all did... I clearly stated 2 genes were identified as having mutated for Lenski's E. coli experiment to yield the Cit+ strain... Honestly, you want me to spell out the contextual specificity for every one of my statements...??? I know you know that I know that you know the association between base pairs, DNA segments and entire genes... we've discussed the matter countless of times... And even if I did include such specificity everywhere you all would further complain about the length of my responses [it's a no-win proposition for me to do so]... (see LnGrrR's satirical response to your other question)...

[Phenomanul]

Well, I too will be out of the forum for several days... I'm sure I'll come back to some more the same...

I know we will never see eye-to-eye on this matter... ah.. C'est la vie!!

Come on over RAIN!!!!

-Peace

[RandomGuy]

I don't agree with this. Specifically because the ~6 million year wasn't a number just thrown into the air, but actually tested by two different methods: immunological antigens and then more recently and with higher precision using molecular genetics from recovered fossils. They both pretty much match in numbers even though they're two pretty distinct methods.



This is were you're confused (wouldn't want to think you were intentionally misleading). You don't need '40 million changes' as in '40 million positive mutations'. Humans have over 3 billion base pairs, but outside of what's called junk DNA, that only makes up 20,000 to 25,000 actual protein coding genes. Meaning, a single mutation (good or bad) on one gene affects more than just a single base pair. You also need to understand that since mutation rate is fairly constant, about half of those changes happened in the human lineage alone.

You also seem to think that organisms don't evolve with gene loss, and that's another concept that's wrong. For example, losing certain gene functionality is reap for selection to act on. Furthermore, losing certain genes can actually change the protein coding in a way that's beneficial for the organism (look up research on the long lost CASPASE12 gene).

There's actually do ented that humans lost roughly 80 genes from the common ancestor with chimps.

Obviously, there's more than just genetic mutations that are involved in evolution. RNA also has a hand with it's own evolution process.



I kid, but you did blast the door open that way. My understanding of your take is that you're proposing a bar of evidence that it's simply unattainable (at least at this point in time), and it's not the same bar used by the scientific community to conduct their research or invalidate their findings. It's a convenient position to put yourself in, but it isn't a position taken by science in general, and I frankly see little reason why anybody else should.

The funny thing is, I found out in my research that the 40 million base pairs figure is used to respond to the common assertion that humans and chimps share 98% or so of our DNA.

"Look we share most of our DNA, that means we are very close relatives"

The creationist rejoinder:

"Oh yeah, we differ by 40 million base pairs, so there, that's a HUGE difference"

Leaving out that 40M is 1.4% of 3.4Bn base pairs.

The point stands.

Given that the VAST majority of human DNA is junk, there is a good chance that most of that is in the junk parts.

The research done since 2001 has narrowed down the differences even more.

Most of the differences have to do with little more than *when* genes get expressed or turned on/off.

A bit longer for thumb development, a bit less for this a bit more for that.

Fascinating stuff, and precisely what one would expect from a common ancestor.

The vast amount of junk is actually one of the things that really reinforces the similarities. Few other animals seem to have as much junk in their DNA trunk as we do. That so much random noise is shared strongly implicates common ancestry.

[ChumpDumper]

That junk was intelligently designed!

[ElNono]

I know you would hate the thought of having to read that article directly from a (gasp!) apologetics website... but I would caution that before you dismiss it consider that most of the quoted researchers in the excerpt above are in fact neoDarwinian Evolutionists... not Creationists...

Have a look here:
http://www.abovetopsecret.com/forum/thread47371/pg12

specifically the posts by amantine back in 2004.

Least you can do is a little research in this stuff. It's a google search away.

[RandomGuy]

I know you would hate the thought of having to read that article directly from a (gasp!) apologetics website... but I would caution that before you dismiss it consider that most of the quoted researchers in the excerpt above are in fact neoDarwinian Evolutionists... not Creationists...

Neat trick quoting "evolutionists". You can quote them all day long and draw all the bad conclusions you want.

More quotes does not equal better arguments, any more than longer DNA strands mean more complex organisms, one of your other rather frequent misstatements.

I could quote Einstein all day long while I am attempting to prove unicorns exist, but that doens't mean that the quotes mean what I say they do, or Einstein ever admitted believing in unicorns.

But I digress. Your attempt to deflect from your previous statements awaits.

[RandomGuy]

Evolution's predictive powers in action.

Either God made our DNA to look like it used to be common with chimps on purpose to with us,

or

Evolution is true.

[RandomGuy]

Going back to the OP (shocking I know)

[RandomGuy]

I have the actual printed article... that online version (which is a revised edition BTW) doesn't include the accompanying graph from where I obtained the "40 million base pair" figure[emphasis mine-RG]...

So exactly what are you callling me out on?

That I can't use a quoted value?

That you feel it is absolutely central to the exercise I introduced?

How convenient for you.

The answer to your question is no, I do not feel it is central to the calculation. It was merely a follow up fact you threw in, that needed to be verified before I would accept it as a given.

[DarrinS]

when I go to Quiznos, I don't really know where the pickles come from, but I just look at my sandwich and know it was intelligently designed.

Well, you could know everything about the organic chemistry of that sandwich, but you would never think those ingredients randomly organized themselves to form a sandwich, would you? I think you unwittingly made a good point.

[DarrinS]

At the end of the day, science can never truly answer the "why?" questions. What we "know" about the world is only models mapped to empirical phenomena.

[RandomGuy]

BTW Lenski's experiment still continues... his current E. coli cultures have reproduced somewhere beyond 50,000 generations from their starting point... That said, the bacteria are all still E. coli and the notable 'change' that allowed his cultures to begin digesting citrate were fully manifest by the 31,500 generation (even if they progressively happened in steps)...

...Think about that for a second [we've done this exercise before]... A couple of genes in an asexual organism were altered after 31,500 generations...

If humans were able to "add" two (or being generous, three) beneficial genes to their genome at this rate, and if we conservatively considered a human generation to be all of 20 years (again generously) then under single lineage dynamics humans would be able to add three beneficial genes to their genome every ~600,000 years!!!

Ummm… that presents quite the conundrum for the accepted evolutionary timeframe of human lineage… especially when one considers there are over 40 million differences between our genome and the chimpanzee ‘next-of-kin’ genome… and if it’s generally accepted that our lineages broke apart only 6 million years ago…

[I know RG will tweak the math and make it all conveniently feasible…]

You mean tweak it like you tweaked it to make it conveniently *unfeasible*?

Let's dissect this here, as I think it is pretty symbolic of the kind and quality of arguments being made.

Facts stated:

1) "Two genes were altered in an asexual organism after 31,500 generations"
2) "there are over 40 million differences between our genome and the chimpanzee ‘next-of-kin’ genome…"
3) "it’s generally accepted that our lineages broke apart only 6 million years ago…"

Assumptions made to complete calculation:

1) Humans and bacteria mutate (add beneficial mutations) at the same generational rate, or 50% more (3 mutations as opposed to 2)
2) a human generation to be all of 20 years

Calculation:
20*31500= 630,000

humans would be able to add three beneficial genes to their genome every ~600,000 years!!!

I will grant, assumption #2, and fact #3.

The rest of it, will require some facts to be confirmed to fully see if this calculation has been "tweaked". I think the fatal assumption in this calculation is the first one, that an asexual bacteria will mutate as fast, generationally speaking, as a sexually reproducing (vive la difference!) human being. It is a very messy, flawed assumption, as far as I can tell.

Bull has been called. Back up fact 1 and 2, and show me on what you base assumption 1.

We will see who is tweaking what.

(edit)
Although it is ultimately YOUR responsibility to back up YOUR claims and assertions. If you can't, or won't, try after a few days, I will do so myself, so don't at me for getting something wrong, when you can't be bothered to back up your claims.

So, going all the way back to this, I will take PM's word that the physical copy of the article he has in his office, different than the online version, supplied him with the figure. So we have fact 3 supported, in some round about way.

PM has also in some round about way stated that bacteria will mutate at a rate much faster than humans for a few reasons, on a per generation basis in any given single lineage. This will make his calculation a bit "generous". I will accede this, as I can buy his given reasons.

Now we get to the difference between "beneficial mutation" and "mutation".

The calculation here concerns "beneficial".

"Beneficial" had a very specific meaning in Lenski's experiment. It meant one thing, and one thing only. Did it increase the ability of the bacteria to reproduce on a medium with citric acid, and digest it.

If that were the ONLY "beneficial" trait that affected genes, that might mean something.

How many other "beneficial" genes were introduced that were not considered part of the experiment?

The environment determines what is "beneficial" and what isn't, for both humans and bacteria.

Evolutionary theory states that selective pressures are the other shaper of change.

Lenski very actively selected for only one trait.

Did past human environments only select for ONE trait and the genes that affected that trait?

Did the bacteria exibit other changes that would, in a more complex environment have also changed genes?

PM himself acknowledged that mutations happen all the time at VERY high rates for bacteria. Gotta get going. That is enough for today.

[RandomGuy]

Well, you could know everything about the organic chemistry of that sandwich, but you would never think those ingredients randomly organized themselves to form a sandwich, would you? I think you unwittingly made a good point.

You are way out of your depth here.

[DarrinS]

You are way out of your depth here.

Do I have to be an accountant, like you, to join the argument? LMFAO. Seems the ability to add and subtract makes one an expert in numerous fields. I believe in evolution. I haven't even been arguing against it, but you are probably smart enough to pick up on that.

[Landon Donofag]

At the end of the day, science can never truly answer the "why?" questions. What we "know" about the world is only models mapped to empirical phenomena.

God of the Gaps

We don't know why, therefore god did it!!

[DarrinS]

God of the Gaps

We don't know why, therefore god did it!!

You completely misunderstood.

[DarrinS]

Life apparently can evolve. Why?

[Proxy]

Life apparently can evolve. Why?

Donnie, shut the up! You're out of your element!