Conference on Evolution

[buffalo]

The tree of one percent

…The biggest branch is the biggest problem

For many biologists concerned with life’s deeper relationships, the longest and most strongly supported branch in many current versions of the tree of life as depicted in Figure 1a or in recent papers 9,16] is also the most misleading: the central branch that implies a sister-group relationship between eukaryotes and archaebacteria 9,13]. It is misleading because at the level of genome-wide patterns of sequence similarity, eukaryotes are far more similar to eubacteria than they are to archaebacteria 56]. Put another way, eukaryotes possess more eubacteria-related genes than they possess archaebacteria-related genes 56,57]. This has escaped the attention of almost everyone, and is one of evolutionary biology’s best-kept secrets, at least in circles where the rRNA tree is thought to speak for the whole genome.

 

[ricmat]

Isn’t it Sherlock Holmes who said, “If you eliminate the impossible, then the possible, no matter how improbable, must be the truth”?

So you have found one possible thing, and everything else is impossible? Are you sure? How can you be sure?

No, because species are always mutating and are never genetically “static”. When a small breeding population breaks away from a larger general population and goes off somewhere to evolve into a new species over the next million years, the larger general population is also evolving over the course of that same million years. So, no matter where you might start in studying species, a million years from now you’re likely to wind up with a set of species totally different from what you started with, and each of these new species will have their own million years’ worth of mutational baggage.

So the answer is…No. You don’t have the smoking gun. But your story is really interesting.

Based on what? Consider how rare an occurrence it must be for two chromosomes to fuse into a working hybrid. Now consider that every member of the human race carries that hybrid chromosome in his/her DNA. The theory that mutations cannot spread throughout a population rapidly is difficult – some would say impossible, even – to maintain once you see the evidence of its having happened.

I’m not saying that if mutations occur that they can’t spread rapidly throughout a population. I am saying that it takes many generations to do so, and advanced life doesn’t breed every few seconds like bacteria, and the populations of pre-humans was small - that’s what you guys say all the time.

Put together an ideal scenario if you wish and run the numbers. Lucy to Mike. How many mutations? How many generations? How long per generation? Assume that every necessary mutation is carried all the way to Mike with no interruption. Run the numbers.

My point is that it makes no sense to use the probability of something’s happening as a justification for denying its having happened when it is already known to have happened. Let’s say that it turned out that the probability my parents would have named me Mike was one in a billion. Your bringing that up wouldn’t change the name on my driver’s license. The most you could say is, “Wow, that was one in a billion!”

I’m not saying you should change the name on your drivers license. I’m saying that it was not inevitable that your name would be Mike, just because your name is Mike.

What I’d like you to say is “Wow, that was one in a billion” (for each mutation). If Mr. X wins the lottery, we all say “how nice.” If Mr. X wins the lottery 10 times in a row we should all be saying “Hey, that wasn’t a random draw! Something intervened here!” I don’t think anyone would say - “Hey, the chances of him winning was 100% because he was the one who won.”

Where you and I part ways, then, is in our respective levels of deference to Church teaching as it pertains to human origins and the origin of life. I start with the science, and when science has run out of possible options, then I’ll see what the Church has to say on the matter. You and Ed seem to start with what the Church says and force science into the constraints of Church teaching. I have no interest in doing that.

–Mike

I’ve stated some of the things that would convince me that evolution really did happen.

Yes, I’ll go with Church teaching in the event of a conflict with science. Lack of obedience is the sin that got us into this mess to begin with, I don’t want to contribute to the mess myself, and I’ll do my best to follow the Church even if I don’t understand it all yet (or if Science doesn’t agree with it all).

 

[buffalo]

Darwin’s bridge between microevolution and macroevolution

“Darwin anticipated that microevolution would be a process of continuous and gradual change. The term macroevolution, by contrast, refers to the origin of new species and divisions of the taxonomic hierarchy above the species level, and also to the origin of complex adaptations, such as the vertebrate eye. Macroevolution posed a problem to Darwin because his principle of descent with modification predicts gradual transitions between small-scale adaptive changes in populations and these larger-scale phenomena, yet there is little evidence for such transitions in nature. Instead, the natural world is often characterized by gaps, or discontinuities. One type of gap relates to the existence of ‘organs of extreme perfection’, such as the eye, or morphological innovations, such as wings, both of which are found fully formed in present-day organisms without leaving evidence of how they evolved.”

 

[buffalo]

**Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods
**

Here, we identified a set of DNA transposon families dubbed SPACE INVADERS (or SPIN) whose consensus sequences are ≈96% identical over their entire length (2.9 kb) in the genomes of murine rodents (rat/mouse), bushbaby (prosimian primate), little brown bat (laurasiatherian), tenrec (afrotherian), opossum (marsupial), and two non-mammalian tetrapods (anole lizard and African clawed frog)

This patchy distribution, coupled with the extreme level of SPIN identity in widely divergent tetrapods and the overall lack of selective constraint acting on these elements, is incompatible with vertical inheritance, but strongly indicative of multiple horizontal introductions.

 

[mpartyka]

So you have found one possible thing, and everything else is impossible? Are you sure? How can you be sure?

Define “everything else.” If “everything else” happens to include some explanation that better fits the data than common descent, let’s hear it. So far the only options I’ve seen pulled from the “everything else” bucket are special creation – doesn’t fit the data – and horizontal gene transfer – novel, but doesn’t fit the data, either.

Put together an ideal scenario if you wish and run the numbers. Lucy to Mike. How many mutations? How many generations? How long per generation? Assume that every necessary mutation is carried all the way to Mike with no interruption. Run the numbers.

That’s like saying, “Show me the odds that such-and-such horse could have won the Kentucky Derby,” when I have the videotape at home that clearly shows such-and-such winning.

If Mr. X wins the lottery 10 times in a row we should all be saying “Hey, that wasn’t a random draw! Something intervened here!”

Probably so. What we would not be saying, however, is, “Mr. X didn’t win 10 times in a row,” because he clearly did.

Lack of obedience is the sin that got us into this mess to begin with…

That’s the interesting thing about this whole discussion. What does common descent tell us about the relationship between sin and death? Thanks to the Bible, most humans have a built-in guilt trip regarding death: “We could have lived forever, but Adam and Eve sinned, so God punished us with death.” But is that really the way it happened? Common descent implies that death was in the world long, long before there existed any creature capable of what we normally think of as “sin.” How does an amoeba sin? And yet countless died before the first human arrived. So, did God create humankind with immortality built-in, or was immortality something God offered to humankind from whatever point in evolution one might call “the beginning”? Do we end up with the same guilt-trip either way? Does “Adam and Eve were created immortal, but by sinning they lost their immortality” functionally amount to the same as “Humanity was created mortal and was given the opportunity by God to be immortal, but by sinning they lost this opportunity”? And even if we do end up in the same place, how are we supposed to feel about having been told the former when it is the latter which appears to have actually happened? All good questions; no good answers as yet.

–Mike

 

[buffalo]

The “Tree of Life” has fallen.

Zombie science: A sinister consequence of evaluating scientific theories purely on the basis of enlightened self-interest

…Zombie science is science that is dead but will not lie down. It keeps twitching and lumbering around so that (from a distance, and with your eyes half-closed) zombie science looks much like the real thing. But in fact the zombie has no life of its own; it is
animated and moved only by the incessant pumping of funds. If zombie science is not scientifically-useable – what is its function? In a nutshell, zombie science is supported because it is useful propaganda to be deployed in arenas such as political rhetoric, public administration, management, public relations, marketing and the mass media generally. It persuades, it constructs taboos, it buttresses some kind of rhetorical attempt to shape mass opinion. Indeed, zombie science often comes across in the mass media as being more plausible than real science; and it is precisely the superficial face-plausibility which is the sole and sufficient purpose of zombie science.

 

[mpartyka]

Buffalo, you’re welcome to post as many articles as you can find on how the evolutionary paths from point A (common ancestor of chimps and humans) to points B1 (chimps) and B2 (humans) aren’t clear, but none of them will provide sufficient justification to deny that the paths exist and were indeed traversed.

–Mike

 

[buffalo]

The Inner Life of the Cell

 

[buffalo]

Buffalo, you’re welcome to post as many articles as you can find on how the evolutionary paths from point A (common ancestor of chimps and humans) to points B1 (chimps) and B2 (humans) aren’t clear, but none of them will provide sufficient justification to deny that the paths exist and were indeed traversed.

–Mike

Thanks! I will continue.

 

[StAnastasia]

I can test gravity right now and as often as I want.

How do you know it’s gravity? Or is that faith?

 

[edwest2]

The “Tree of Life” has fallen.

Zombie science: A sinister consequence of evaluating scientific theories purely on the basis of enlightened self-interest

…Zombie science is science that is dead but will not lie down. It keeps twitching and lumbering around so that (from a distance, and with your eyes half-closed) zombie science looks much like the real thing. But in fact the zombie has no life of its own; it is
animated and moved only by the incessant pumping of funds. If zombie science is not scientifically-useable – what is its function? In a nutshell, zombie science is supported because it is useful propaganda to be deployed in arenas such as political rhetoric, public administration, management, public relations, marketing and the mass media generally. It persuades, it constructs taboos, it buttresses some kind of rhetorical attempt to shape mass opinion. Indeed, zombie science often comes across in the mass media as being more plausible than real science; and it is precisely the superficial face-plausibility which is the sole and sufficient purpose of zombie science.

Thank you, Buffalo. Some think that science, a wholly human activity performed by human beings, is pure as the driven snow. But any enterprise populated by human beings is subject to corruption. The fatal flaw called sin drives too many of us to accept money, fame, prestige, or whatever, to satisfy a temporal desire.

Propaganda is an ages old weapon designed to get ‘the enemy’ to do the wrong thing, always to your advantage.

Right now, the big deception is science. It has been thoroughly politicized. If you don’t believe in it, you, and/or your political party, are whitewashed into the “all you believe is belief” camp. Right there with the dreaded Findamentalists. Far be it from me to say anything nice about America’s enemies but creating villains out of politicians in the US is old hat. The current deception is Science v Belief. In this corner, Science, well regarded by the crowd, heavily promoted, the favorite – after all, the story goes, he represents truth, reason and evidence until you look (as Buffalo just did) just under the surface and find the same corrupting influences sometimes getting him to say things that aren’t entirely true.

Don’t be deceived. Deception is the devil’s number one weapon.

Peace,
Ed

 

[zachforn]

Thank you, Buffalo. Some think that science, a wholly human activity performed by human beings, is pure as the driven snow. But any enterprise populated by human beings is subject to corruption. The fatal flaw called sin drives too many of us to accept money, fame, prestige, or whatever, to satisfy a temporal desire.

Propaganda is an ages old weapon designed to get ‘the enemy’ to do the wrong thing, always to your advantage.

Right now, the big deception is science. It has been thoroughly politicized. If you don’t believe in it, you, and/or your political party, are whitewashed into the “all you believe is belief” camp. Right there with the dreaded Findamentalists. Far be it from me to say anything nice about America’s enemies but creating villains out of politicians in the US is old hat. The current deception is Science v Belief. In this corner, Science, well regarded by the crowd, heavily promoted, the favorite – after all, the story goes, he represents truth, reason and evidence until you look (as Buffalo just did) just under the surface and find the same corrupting influences sometimes getting him to say things that aren’t entirely true.

Don’t be deceived. Deception is the devil’s number one weapon.

Peace,
Ed

If science is deception, I guess deception got you your computer constructed, deception split the atom (or do you not believe that Hiroshima occurred?), deception created laser equipment, deception understands DNA enough to convict rapists and murders, deception launched space exploration, this list could go on and on and on.

Look around you, most items of modern American culture (EVERYthing using plastics) are science applied. When you look around and see this stuff, do you think in your head that you’re being deceived in seeing and using them. Is Satan fooling you into thinking you are using a computer right now?

Again, some Catholics want all the conveniences sciences gives them, but then totally want to dismiss it when it starts to step on their beliefs.

Or am i just obscuring the issue with what is obvious. As soon as you stop using the benefits of science, then you can start to criticize it, how about that.

 

[Namesake]

T But any enterprise populated by human beings is subject to corruption.

Peace,
Ed

That’s just way too easy Ed, and I bet you fully understand that idea.

 

[edwest2]

For those who do not believe that science is the current weapon of choice, I offer the following:

krestaintheafternoon.blogspot.com/2009/05/chris-matthews-sets-up-ultimate-straw.html

Peace,
Ed

 

[ricmat]

It’s amusing to see everyone arguing about the validity of science, yet everyone on this forum uses their computers, televisions, cell phones…

Do you not understand that THE EXACT SAME SCIENTIFIC METHOD that got you your fun little computer and tv and cell phone is the same science that seems to want to be dismissed.

Well, I’ve designed computers, and industrial robots, and some other stuff like that. How about you?

The EXACT same science procedures that produced our understanding of the electromagnetic force, the behavior of molecules and atomic particles, the behavior of orbiting spheres, the launch capabilities to put satellites in orbit and ALL of SCIENCE that came before us, ALL OF IT CONTRIBUTED to your computer that you are using right now.

Really! WOW! I didn’t know that. (Actually, I did).

Do you deny that you are using a computer right now?!? How do you think that computer got here? Science. The exact same science that seems to be under attack, or at the very least, is being misrepresented in this thread.

If you don’t believe in science, DNA, theories of evolution, atomic structures, TURN OFF YOUR COMPUTER, because your playing on something you don’t believe in.

It’s wonderful how some catholic can pick in choose what science to believe in. As long as it’s useful to them (computers, tv, cell phones) they believe it. As soon as it’s not, it’s a Lie, evil, illusion. etc.

Computers, electronics, etc. are based on science that is a result of reproducible experiments, not fantasy speculations.

 

[ricmat]

If science is deception, I guess deception got you your computer constructed, deception split the atom (or do you not believe that Hiroshima occurred?), deception created laser equipment, deception understands DNA enough to convict rapists and murders, deception launched space exploration, this list could go on and on and on.

Look around you, most items of modern American culture (EVERYthing using plastics) are science applied. When you look around and see this stuff, do you think in your head that you’re being deceived in seeing and using them. Is Satan fooling you into thinking you are using a computer right now?

Again, some Catholics want all the conveniences sciences gives them, but then totally want to dismiss it when it starts to step on their beliefs.

Or am i just obscuring the issue with what is obvious. As soon as you stop using the benefits of science, then you can start to criticize it, how about that.

Because some science can successfully produce workable devices, does not mean that everything which is termed science is as successful.

 

[dixieagle]

This is a good thing to point out, Namesake. However, to augment what you say, perhaps it would be helpful to distinguish between two categories of belief, namely, “belief that” and “belief in.” The former involves notional assent to a proposition. Acceptance of the theory of evolution on the basis of the evidence marshalled in its favour is certainly equivalent to “belief that evolution is true.”

“Belief in,” however, carries connotations of personal trust. of placing our confidence in a person, an institution, an idea, a principle, a faith, or a deity. I don’t know of any evolutionists who claim to put their faith in Charles Darwin as one who is possessed of saving power.

As for me, I believe in God, and I believe that evolution is the best current explanation of biological diversity on Earth.

StAnastasia

As the MIL of a newly minted (and thoroughly Catholic) Ph.D. in evolutionary biology… very well put.

 

[edwest2]

There’s more to being Catholic than a Ph.D.:

bringyou.to/apologetics/p81.htm

Pope Benedict XVI

Monod nonetheless finds the possibility for evolution in the fact that in the very propagation of the project there can be mistakes in the act of transmission. Because nature is conservative, these mistakes, once having come into existence, are carried on. Such mistakes can add up, and from the adding up of mistakes something new can arise. Now an astonishing conclusion follows: It was in this way that the whole world of living creatures, and human beings themselves, came into existence. We are the product of “haphazard mistakes.”

What response shall we make to this view? It is the affair of the natural sciences to explain how the tree of life in particular continues to grow and how new branches shoot out from it. This is not a matter for faith. But we must have the audacity to say that the great projects of the living creation are not the products of chance and error. Nor are they the products of a selective process to which divine predicates can be attributed in illogical, unscientific, and even mythic fashion. The great projects of the living creation point to a creating Reason and show us a creating Intelligence, and they do so more luminously and radiantly today than ever before. Thus we can say today with a new certitude and joyousness that the human being is indeed a divine project, which only the creating Intelligence was strong and great and audacious enough to conceive of. Human beings are not a mistake but something willed; they are the fruit of love. They can disclose in themselves, in the bold project that they are, the language of the creating Intelligence that speaks to them and that moves them to say: Yes, Father, you have willed me.

Peace,
Ed

 

[ricmat]

“Belief in,” however, carries connotations of personal trust. of placing our confidence in a person, an institution, an idea, a principle, a faith, or a deity. I don’t know of any evolutionists who claim to put their faith in Charles Darwin as one who is possessed of saving power.

Not saving power, but we do seem to see a lot of evolutionists who put their faith in Charles Darwin as one who is possessed of a truth contrary to Catholic teaching.

 

[Michaelo]

Darwin’s bridge between microevolution and macroevolution

“Darwin anticipated that microevolution would be a process of continuous and gradual change. The term macroevolution, by contrast, refers to the origin of new species and divisions of the taxonomic hierarchy above the species level, and also to the origin of complex adaptations, such as the vertebrate eye. Macroevolution posed a problem to Darwin because his principle of descent with modification predicts gradual transitions between small-scale adaptive changes in populations and these larger-scale phenomena, yet there is little evidence for such transitions in nature. Instead, the natural world is often characterized by gaps, or discontinuities. One type of gap relates to the existence of ‘organs of extreme perfection’, such as the eye, or morphological innovations, such as wings, both of which are found fully formed in present-day organisms without leaving evidence of how they evolved.”

More irreducible complexity?

This is the quintessential example of the argument from incredulity. The source making the claim usually quotes Darwin saying that the evolution of the eye seems “absurd in the highest degree”. However, Darwin follows that statement with a three-and-a-half-page proposal of intermediate stages through which eyes might have evolved via gradual steps (Darwin 1872).

* photosensitive cell
* aggregates of pigment cells without a nerve
* an optic nerve surrounded by pigment cells and covered by translucent skin
* pigment cells forming a small depression
* pigment cells forming a deeper depression
* the skin over the depression taking a lens shape
* muscles allowing the lens to adjust

All of these steps are known to be viable because all exist in animals living today. The increments between these steps are slight and may be broken down into even smaller increments. Natural selection should, under many circumstances, favor the increments. Since eyes do not fossilize well, we do not know that the development of the eye followed exactly that path, but we certainly cannot claim that no path exists.

Evidence for one step in the evolution of the vertebrate eye comes from comparative anatomy and genetics. The vertebrate βγ-crystallin genes, which code for several proteins crucial for the lens, are very similar to the Ciona βγ-crystallin gene. Ciona is an urochordate, a distant relative of vertebrates. Ciona’s single βγ-crystallin gene is expressed in its otolith, a pigmented sister cell of the light-sensing ocellus. The origin of the lens appears to be based on co-optation of previously existing elements in a lensless system.

Nilsson and Pelger (1994) calculated that if each step were a 1 percent change, the evolution of the eye would take 1,829 steps, which could happen in 364,000 generations.

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