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Thursday, April 28, 2016

Fun and games with Otangelo Grasso about photosynthesis

Otangelo Grasso just posted another one of his screeds. This time it's on photosynthesis. All of his "essays' conform to the same pattern. He looks for some complex set of biochemical reactions, usually in complex animals, then claims that it couldn't possibly have evolved because the whole thing is irreducibly complex according to his understanding of biochemistry and evolution.

It's a classic argument from ignorance.

In this case it's photosynthesis in flowering plants. He posted this figure from the Kegg database ....


Then he says,
In photosynthesis , 26 protein complexes and enzymes are required to go through the light and light independent reactions, a chemical process that transforms sunlight into chemical energy, to get glucose as end product , a metabolic intermediate for cell respiration. A good part of the protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is a interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someone rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage, all happened by a series of natural events that we can call ad hoc mistake "formed in one particular moment without ability to consider any application." , to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to " feed " ATP synthase nano motors to produce ATP , and so on ? Such independent structures would have not aided survival. Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. If this mechanism would not work starting right from the beginning, various radicals and active oxygen species with harmful effects on photosystem II (PSII) would make it cease to function. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.
I responded on Facebook, pointing out that the cytochrome bc complex and ATP synthase pre-date photosynthesis [Facebook: Photosynthesis]. I also pointed out that there are many living species that use only simpler versions of photsystem I or only photosystem II to carry out photosynthesis [e.g. A Simple Version of Photosynthesis]. Those nasty little facts don't seem to fit with his claim that, "In these systems, nothing works until all the necessary components are present and working."

I probably should have known better. Otangelo Grasso's standard response to such criticism is to avoid dealing directly with his false statements and shift the goalposts on to some other topic. He then posts all kinds of links to websites that seem to back up his claims even if they have nothing to do with the criticisms. You can see him at work on the Facebook thread.

It's pretty frustrating. I probably shouldn't respond to kooks, especially those who think they are experts in biochemistry.


277 comments :

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Anonymous said...

BC writes, "when . . . you base your argument on an assumption that evolution is true, the argument appears circular to [me]."

BC, once the acceleration due to gravity is determined, we can use that value to determine where a projectile with certain characteristics will land. We don't have to determine it again for each projectile. This is true for scientific ideas in general.

The reality of evolution is abundantly supported by careful lines of reason involving comparative morphology, comparative DNA sequences, biogeography, fossils, population genetics, etc. (See Why Evolution is True for a clear presentation of basic evidence.) Therefore, I can use evolution to explain many other observations in biology. I don't need to prove it again each time.

In the case of the blood clotting cascade, my goal is not so lofty as the proof of evolution. It is merely to show that the blood clotting cascade is actually consistent with evolution, although blood clotting is called "irreducibly complex." How?

On the theoretical side, we figure out that any given biochemical process could, through evolution, become more complex. To start with, enzyme A does a job. At some point, enzyme B helps. More changes occur and enzyme B becomes essential. The process can repeat with additional enzymes. Eventually, in some species, Enzymes A, B, C, and D may become necessary to do that job, and we could call it "irreducibly complex." Nice idea, but how to find evidence? The idea predicts that we would see different species that have different enzymes involved in the process, and that the observations would be consistent with phylogeny (evolutionary history, geneology). Do we see that?

Observations: Different vertebrates do have different numbers of enzymes involved in blood clotting. Lampreys have just one. When we map the observations onto known phylogeny (including the inference from other evidence that lampreys and humans have a common fishy ancestor), we see that the blood clotting enzymes fit well.

Therefore, we see that the "irreducible complexity" of the blood clotting mechanism in humans fits into evolutionary theory well. It is not a problem for evolution.

Unknown said...

No.1. Any evidence to back up your claim ?

No.2. How do you possibly know ?

No.3. Your point ?

No.4. "So claiming that the overall equation for photosynthesis is production of a 6-carbon sugar is misleading in more ways than one."

I have nowhere made this claim.

No.5. Does not contradict anything i said.

" Storage of chemical energy in the form of glucose/starch/cellulose is a later adaptation "

How do you know its a later adaptation ?

No.6. Again, no evidence to back up the claim is provided. Its a just so story .

Tom, you have not provided any more compelling naturalistic explanation of anything i presented.

Anonymous said...

Tom, looks like a good start to me.

Unknown said...
This comment has been removed by a blog administrator.
Jmac said...

Produce empirical evidence that incipient stages of any 'irreducibly complex' system were not advantageous.

Shouldn't it be the other way around Chris B? Shouldn't the evolution supporters provide empirical evidence for their claims in the first place? If they don't have any evidence for their claims, not to mention empirical, on what are their claims based? Just so stories? Or perhaps: "evolution is a fact so this issue is a fact too".

Grasso, this is as much as you are going to get from "scientists" who support a "scientific theory" that doesn't meet any requirements of a scientific theory.

How is this possible in 21st century? I wonder...

Hmmm... Not anymore ...

Unknown said...
This comment has been removed by the author.
Faizal Ali said...

I may have ideological bias but I am truly trying to understand the science.

You can't be trying very hard, because you still don't understand it, despite assistance from respected scholars like Larry Moran and Joe Felsenstein, among several others.

IMHO you are not or you would be arguing wo ad hominem attacks. You seem so sensitive to challenges to TOE it must more than science your interested in.

You call the nonsense you post "challenges"? They aren't. The challenge is getting thru your denial to impart some knowledge.

Why don't you go to other sites where you get challenged?

Well, I tried posting on Uncommon Descent, but was banned shortly thereafter. I guess they don't like to be challenged there.

Bill Cole said...

lutesuite
"Well, I tried posting on Uncommon Descent, but was banned shortly thereafter.I guess they don't like to be challenged there"

Try the skeptical zone. If you want to see how you do as minority try darwin's god. If you make arguments I will try to understand them and will agree if you supply solid evidence.

I agree with many of Larry and Joe's arguments. In his argument with Otangelo I understood and agreed with Larry's position. Tom and
BW on the other hand were making circular arguments IMHO.

Bill Cole said...

BWilson
BC, once the acceleration due to gravity is determined, we can use that value to determine where a projectile with certain characteristics will land. We don't have to determine it again for each projectile. This is true for scientific ideas in general"
Good example here. Since the know force you are modeling is gravity you can create a mathematical model for the behavior for a projectile and the empirically test it enough times to come out with a predictive model.

How would you model specie A transitioning into specie B?

Tom Mueller said...

FTR - the compilation above would constitute blatant plagiarism if I were not to acknowledge Lawrence Moran as my source and inspiration.

I shall set an example for Otangelo Grasso when I compose my final version, by modeling how to do just that.

Before taking my leave and going to bed - I just want to conclude by acknowledging and paraphrasing Larry's first rebuttal to Otangelo Grasso (to confirm I got it all correct)

Let's presume true that various constituent proteins in some complex component of photosynthesis (OEC for example) were individually non-functional.

That observation would not constitute proof positive that any such component could therefore not have arisen by natural means.

This final observation is moot. Otangelo has not even managed to identify any such non-functional proteins in any such complex.



Anonymous said...

BC, I responded to your complaint about circular arguments to explain that my argument was not circular. You don't respond to that. I assume because you realize you were wrong and you'd never admit that?

Considering the diversity of events that can lead to the evolution of species B from species A, asking for an empirical model of it makes as much sense as asking for an empirical model of the revolutionary war. So no, I don't have one.

I do, however, have the fact that sudden evolution of one plant species from another by polyploidization had been observed more than once. Better than any model, wouldn't you agree?

Like the words deer and sheep, the word "species" is spelled the same way whether plural or singular. "Specie" is a financial term referring to coins.

Unknown said...

Tom Mueller

sorry, not engaging further. Larry is deleteing my posts deliberately.

Chris B said...

Eric,

"Shouldn't it be the other way around Chris B? Shouldn't the evolution supporters provide empirical evidence for their claims in the first place?"

No Eric, because Otangelo is making the specific claim that IC systems cannot be produced by evolution. He is making the claim here. Evolutionary theory has several plausible mechanisms by which IC systems can evolve without any help from a magical being.

'Plausible' you will pounce on: plausible is not evidence. And you are right. But therein lies the flaw in the IC argument. ID/creationists deliberately choose highly complex, ancient systems like flagellae and photosynthesis, not because they are the best examples of IC systems. Rather, they choose systems so deep in time that it would be impossible to empirically demonstrate the actual evolutionary pathway that led us to extant IC systems. How could anyone know the all the contingent and chance-prone events that lead us to today's many different forms of flagellae and photosynthetic pathways? I can't, and neither can you or Otangelo. You can't trace your lineage back to your African progenitors. That doesn't mean you are not a Homo sapiens. Asserting this as evidence in favor of your ID/creationist hypothesis is therefore nothing but a god-of-the-gaps argument from ignorance (re-read Larry's blog post that we are all posting to - it's right there).

All of Otangelo's Gish gallop about photosynthesis is just to distract everyone from some obvious implications of his argument, and to keep the burden of proof on his opponents, without ever having to provide a shred of evidence in favor of his ID/creationist fantasies.

However, in order for IC systems to be impossible to evolve by modern evolutionary theory, you would have to show that all incipient stages of evolution in those systems had no useful function in any capacity. Thus the double edged nature of Otangelo's dishonest argument is revealed. ID/creationists cannot demonstrate any such thing.

"If they don't have any evidence for their claims, not to mention empirical, on what are their claims based? Just so stories? Or perhaps: "evolution is a fact so this issue is a fact too"."

Stop projecting, Eric. You assume a magical being did it without any empirical evidence or even just so stories, but only because you assert it as fact. You have ZERO positive evidence for ID/creationism. And look through Otangelo's posts. When you strain out all the logical fallacies and evidence-free assertions, every single fact sifted out has been discovered by scientists collecting empirical data without resorting to magical beings to explain their observations.

"Grasso, this is as much as you are going to get from "scientists" who support a "scientific theory" that doesn't meet any requirements of a scientific theory."

Grasso has gotten far more time and attention than his recycled arguments, debunked decades ago, deserved.

"How is this possible in 21st century? I wonder..."

Because in the 21st century, irrational religious beliefs still blind otherwise rational people to reality.

Larry Moran said...

I will not delete any posts where you actually "engage." I will delete posts that copy-paste irrelevant material (often plagiarized) from one of your websites.

I'm not convinced that you really know how to engage in a serious discussion.

Unknown said...

You have always a excuse for your disastrous moderating behavior, Larry.

Faizal Ali said...

BWilson
BC, once the acceleration due to gravity is determined, we can use that value to determine where a projectile with certain characteristics will land. We don't have to determine it again for each projectile. This is true for scientific ideas in general"
Good example here. Since the know force you are modeling is gravity you can create a mathematical model for the behavior for a projectile and the empirically test it enough times to come out with a predictive model.

How would you model specie A transitioning into specie B?


Bad analogy. Here's a better one:

Geologists believe that the shapes of mountains are determined by factors such as tectonic forces and erosion. Given this, how would they model the production of a mountain with a specific form, such as the Matterhorn or Mt. Kilimanjaro? i.e. If a geologist with modern scientific knowledge lived 200 million years ago, would he have been able to predict the precise shape these mountains would take? If not, does that mean the shapes of mountains are actually created by an intelligent designer?

Bill Cole said...

BWilson
BC, I responded to your complaint about circular arguments to explain that my argument was not circular. You don't respond to that. I assume because you realize you were wrong and you'd never admit that?

Considering the diversity of events that can lead to the evolution of species B from species A, asking for an empirical model of it makes as much sense as asking for an empirical model of the revolutionary war. So no, I don't have one."

Your argument upfront assumes fish to man common decent. If you opponent agrees than there issues no problem but if he doesn't you first need to establish the common decent if you are going to use it.

Your point on the difficulty of modeling the event is right. I applaud the examples you supplied as evidence. The overarching theory requires some very complex biochemical transitions and I am really struggling to figure out how except throwing against the wall lot of potential ways a genome can change and hoping something will stick. Unfortunately wo a mechanism there isn't an overall theory.

Bill Cole said...

Lutesuite

Geologists believe that the shapes of mountains are determined by factors such as tectonic forces and erosion. Given this, how would they model the production of a mountain with a specific form, such as the Matterhorn or Mt. Kilimanjaro? i.e. If a geologist with modern scientific knowledge lived 200 million years ago, would he have been able to predict the precise shape these mountains would take? If not, does that mean the shapes of mountains are actually created by an intelligent designer?"
Design is an inference argument and in your case I would not infer design because the cause(s) of the shape of the mountains are known.

Anonymous said...

BC, you wrote, "Your argument upfront assumes fish to man common decent. If you opponent agrees than there issues no problem but if he doesn't you first need to establish the common decent if you are going to use it."

My argument about evolution of blood clotting was not circular, because the common descent of all vertebrates was established long ago (ca. 150 years ago) and has been confirmed multiple times since (e.g. with DNA phylogenies). It is a well established fact, available to use in other discussions. Your inadequacy in this field does not somehow make my argument circular.

If you want to cure this inadequacy, you could read a book that covers many aspects of basic evolution theory, such as a well-written evolution textbook like "The Tangled Bank" by Zimmer or a book for non-scientists such as "Why Evolution is True." This wouldn't work for many of the creationist commentators here, but you don't seem to be stupid, just uninformed.

Unknown said...

bwilson295-
The ‘creationist’ thinks the universe is a creation from a conscious being.
In that case, one would expect a ‘why’ question to be answered with an intention or reason.
(I’m not suggesting that premise need be correct, I’m just talking about the logical consequences of accepting that premise).

“Why did you take the money?”
“I took the money because my elbow extended causing my hand to reach to the pile of money and then my fingers clasped around the money. My elbow then bent back and my legs began to move. That’s why I took the money.”

We want an ‘intention’ or ‘reason’ from a conscious entity. If I claimed I thought the money was mine, then why I took it would be clear: I intentionally did it for the reason it was mine. No amount of ‘how’ will satisfy in the same way.

If the universe is a creation, then all the ‘how’ answers to the ‘why’ questions look like ‘motivated stopping’ from a ‘question begging’ person who is in denial about the most important aspect of reality.

You keep tying this to what is ‘emotionally satisfying’ and fail to see the logic from the standpoint of someone who has the premise the universe is a creation.

Unknown said...

Grasso-
I have no faith in evolution.
The rejection of Darwin’s proposal as outlined in the quote you give is called ‘modern evolutionary theory'.

Faizal Ali said...

Design is an inference argument and in your case I would not infer design because the cause(s) of the shape of the mountains are known.

You've avoided answering the full question: Do you believe geologists should be able to predict the exact shape a mountain will take 200 million years from now, since (as you agree) the mechanisms by which mountains are formed are known?

Larry Moran said...

And you always have an excuse for spamming my blog.

Anonymous said...

JJ -- You're right as far as you go. A person asks who "why" question generally is looking for an answer involving intention or reason, so he's going to be unsatisfied with a "how" answer.

The problem is, what if there is no "why" answer? No intention or reason?

Then the person will keep being unsatisfied and no doubt will think the problem was with the person answering the question as best he can. However, the real problem was with asking the "why" question where it didn't apply.

Unknown said...

Don't worry, if that is the problem, there is a solution......

Jmac said...

Otangelo,

Larry is the host of this blog and there is not much you can do to change it. He is in charge, I'm afraid...

You are following the path of quite a few who challenged Larry and many other Darwin faithful over the years on his blog. They have all been treated the same way you have; more or less.

You, on the other hand, though probably having good intentions, have allowed Larry to find an excuse to remove your posts. Whether they are legit reasons or not now, because of your not so legit actions on your part, all you can hope for is that the public opinion of many, many people who read Larry's blog will sympathise with you. That's is pretty much all you can hope for from now on, I believe...

If you are a religious man; if you believe in the bible, you would probably never be surprised by how you were treated on this blog.

Jmac said...

BTW: I was just reviewing some of my favourite re-posts, and I don't really know if this is the right channel or way to broadcast this, but I seem to have notice that Larry Moran disagrees with Dawkins opinion that the design in life is not apparent-"life has the appearance of design" I don't know what Larry is trying to say, but I don't think Dawkins will like it...

Bill Cole said...

BW
My argument about evolution of blood clotting was not circular, because the common descent of all vertebrates was established long ago (ca. 150 years ago) and has been confirmed multiple times since (e.g. with DNA phylogenies). It is a well established fact, available to use in other discussions. Your inadequacy in this field does not somehow make my argument circular."

Saying this is a fact is quite a statement. I guess this is why you are blinded by your bias. Not everyone agrees this is a fact but non the less you will do fine with people who agree with your presumptions. Good luck with persuading people who live outside your worldview when you make factual claims about events in the distant past that you have not been able to measure or observe.

Bill Cole said...

lutesuite

"You've avoided answering the full question: Do you believe geologists should be able to predict the exact shape a mountain will take 200 million years from now, since (as you agree) the mechanisms by which mountains are formed are known?"

I honestly don't know what level of prediction they could make given the current state of advance climate models.

Faizal Ali said...

@ Bill Cole:

I don't know if you're trying to be funny, or if you are actually that ignorant. However, to play it safe: Geologists are not able to predict the precise shape mountains will take millions of years in the future.

So, with that valuable piece of insight now yours, I will rephrase my question: If geologists understood the processes by which mountains are formed, should they be able to predict the precise shape a specific mountain will take millions of years in the future? And, since they are not able to do so, does this not mean that they do not understand how mountains are formed, and that what you call "the design inference" is actually a better explanation?

Bill Cole said...

Lutesuite
"So, with that valuable piece of insight now yours, I will rephrase my question: If geologists understood the processes by which mountains are formed, should they be able to predict the precise shape a specific mountain will take millions of years in the future? And, since they are not able to do so, does this not mean that they do not understand how mountains are formed, and that what you call "the design inference" is actually a better explanation?"

Again, the design inference is used to identify the "high level" cause of an observed result. It is an inference to a competing hypothesis, If you and I took a trip to Colorado and were having a beer looking at the grand canyon you could hypothesize that wind and water erosion formed it and I could hypothesize it was design. I think we would chat and agree that your hypothesis was most likely the right one. This is not about prediction it is about assigning cause to something observed. If we were in your situation and needed to make a prediction about what the mountain will looked like 200 million years from now then we would need a model to make that prediction. Design inference and prediction are different animals. Also, design inference is not a mechanism so it lacks predictive power. This is the mistake Steven Meyer made in the debate Larry saw in Toronto when he said intelligent design could predict junk DNA. The design inference does not predict anything because it is not a mechanism. To make it predictive we would need to peel the onion with how questions but this is beyond the science at this point.

John Harshman said...

If you and I took a trip to Colorado and were having a beer looking at the grand canyon

That must be one of those new Colorado pot-laced beers.

Faizal Ali said...

@ Bill Cole:

This is not about prediction it is about assigning cause to something observed.

And yet you demand that evolutionary biologists be able to predict which species will result from evolution in the future.

This sort of intellectual dishonesty and hypocrisy is why many here doubt that you are engaging in honest discussion.

judmarc said...

but I am truly trying to understand the science

Nope. If you were, then you would have taken the opportunity to discuss my satisfactory answer to your challenge to show a correct experimental prediction for evolutionary biology. Or do you think Shubin just managed a lucky shot?

Unknown said...
This comment has been removed by the author.
Faizal Ali said...

We could also include the human chromosome 2 fusion as a successful prediction of evolutionary theory.

One could ask Bill Cole for counter examples of successful predictions from intelligent design, but he has already attempted to head that off by conceding that ID is a hypothesis that cannot be used to make predictions. One has to wonder how something could be a hypothesis without generating predictions. And no, Bill, the problem does not magically disappear if you mislabel your "hypothesis" as an "inference."

Tom Mueller said...

I have collected some salient quotes from Bill Cole, and I must say I am most amused by his own circular definition of “circular argument”


BC: My point really is simply to say that when you are arguing with someone is skeptical and you base your argument on an assumption that evolution is true, the argument appears circular to the person you are trying to convince.

BC: "Your argument upfront assumes fish to man common decent. If you opponent agrees than there issues no problem but if he doesn't you first need to establish the common decent if you are going to use it."

BC: Saying this [ the common descent of all vertebrates was established long ago] is a fact is quite a statement. I guess this is why you are blinded by your bias. Not everyone agrees this is a fact but non the less you will do fine with people who agree with your presumptions. Good luck with persuading people who live outside your worldview when you make factual claims about events in the distant past that you have not been able to measure or observe.

Bill Cole's rejoinders reminds me of a previous debate regarding dynamics of the celestial spheres and the celestial firmament as described in the Bible.
https://en.wikipedia.org/wiki/Dynamics_of_the_celestial_spheres

Here is the relevant quote from the wikipedia article:

Johannes Kepler's (1571–1630) cosmology eliminated the celestial spheres, but he held that the planets were moved both by an external motive power, which he located in the Sun, and a motive soul associated with each planet. In an early manuscript discussing the motion of Mars, Kepler considered the Sun to cause the circular motion of the planet. He then attributed the inward and outward motion of the planet, which transforms its overall motion from circular to oval, to a moving soul in the planet since the motion is "not a natural motion, but more of an animate one". In various writings, Kepler often attributed a kind of intelligence to the inborn motive faculties associated with the stars.

In the aftermath of Copernicanism the planets came to be seen as bodies moving freely through a very subtle aethereal medium. Although many scholastics continued to maintain that intelligences were the celestial movers, they now associated the intelligences with the planets themselves, rather than with the celestial spheres.


Sound familiar?

Tom Mueller said...

It would appear that anybody who endorses Newton’s Three Laws of Motion is ipso facto similarly guilty of ‘circular reasoning”, according to Bill Cole’s definition!

Let’s examine Bill Cole’s understanding of circularity more closely:

A scientist would prefer to invoke Okham’s razor, when suggesting that no supernatural intervention need be invoked if and when a natural explanation can be found.

The only “presumption” on the part of modern science is that natural explanations can be found for natural phenomena; all scientists need do, is look.

Let's presume for the sake of argument that it is in fact possible to believe in Intelligent Design and be a scientist.

An honest scientist will acknowledge data that contradict his original hypothesis (ID let's say) and publically admit when his original ID hypothesis can no longer best explain the data.

Meanwhile, many religious other folk do not dispute the scientific “presumption” of natural phenomena having natural causes and see no contradiction therein with “faith”. So-called Theists would be one example. Even Roman Catholics since Thomas Aquinas (perhaps better yet since Galileo) would also agree with “scientific presumption” as just defined. (cf Dawkins friendly exchange with Father Coyne, former director of the Vatican Observatory)

Bill Cole would not.

Bill is most disingenuous by suggesting Barb and her ilk are "blinded" by a particular “worldview” while ignoring the salient fact that all thinking human beings have a world view including himself.

The debate then descends into a shouting match of “science is faith” vs “no it is not”.

Here is how modern Geology evolved:

The Biblical presumption was that the planet is relatively young. Much evidence accumulated obliging even G-d fearing and pious Christian scientists to reluctantly subscribe to the heresy that contradicted a literal interpretation of the Bible. (Lyell would be a case in point)

Here is how modern Biology evolved:

The Biblical presumption was that the planet is relatively young and species were created by God as we currently find them. Much evidence accumulated obliging even G-d fearing and pious Christian scientists to reluctantly subscribe to the heresy that contradicted a literal interpretation of the Bible. (Darwin who enrolled Charles at Christ's College, Cambridge intending to become an Anglican parson; would be another case in point)

In fact the progress of evolutionary theory is punctuated by the insights of devoutly religious individuals whose default setting was that G-d is real directly impacting human lives (Dobzhansky and Ayala would be two more cases in point)

In short, Bill Cole's presumption of scientific presumption is untenable to say the least; and more than disingenuous, it is intellectually dishonest!

Tom Mueller said...

Back to modern humans and modern fish sharing a common ancestor:

Evidence?

The most direct evidence would be Paleontology together with Molecular Genetics (fossil DNA) as brilliantly elucidated in Neil Shubin’s book (as already mentioned on more than one occasion above)

Let’s summarize the Photosynthesis debate so far:

Creationists have attempted to suggest that Intelligent Design is obvious for three reasons:

1 - Photosyntesis as one example is “as a whole” irreducibly complex
2 - Even if Behe’s definition of Irreducible Complexity does not apply to Photosyntesis “as a whole”, individual components of photosynthesis (OEC, PI PII) are irreducibly complex.
3 - Irreducible Complexity can ONLY be ascribed to Intelligent Design and never to Natural causes.

All three shibboleths have been slain.

Photosynthesis can be explained by natural causes and in fact is in fact possessed of a pretty UNintelligent design! RuBisCo has an incredibly high Km and is prone to bind O2 instead of CO2 in futile and wasteful cycles called photorespiration that can best be explained by understanding RuBisCo

1 - represents NO adaptive peak and
2 – can best be understood to have first evolved when atmospheric Oxygen levels were low.

If Bill Cole still persists in disagreeing, he must acknowledge that HE IS BURDENED with an anachronistic “WORLD VIEW” and that the burden of proof now rests with him to explain how:

1 - Newton is incorrect and angels really push the planets in their orbit, and while he is at it
2 - Evolution is still not the best explanation for photosynthesis; but rather some very inefficient, less than perfectly adapted and clearly less than intelligent design version of photosynthesis can better explain the data presented so far.

Bill Cole’s explanation must accommodate the fossil record:

1 – as data amassed by paleontology
2 – as data amassed by Geneticists i.e. non-functional junk “fossil DNA” in plant (not to mention fish and human genomes) that mirror and pace the paleontological story

Tom Mueller said...

The point is moot - I would prefer not to engage with you further in any case

Anonymous said...

BC, you're right that the blood clotting example and the photosynthesis example would never convince a person of the truth of evolution unless that person already understood evolution. Without that deeper understanding, he'd never grasp what was wrong with the anti-evolution arguments. The problem here isn't circular arguments so much as self-reinforcing ignorance.

However, I'd never use those complex biochemical examples to demonstrate evolution to a beginner. I'd use the way biodiversity clusters into groups (convincing to people who actually see that biodiversity but not the average person), comparative morphology, what I know about geology and fossils, and some other obvious examples.

You're not stupid. If you really were "trying to understand the science" you'd begin with material geared to your level of understanding and you would come to understand the science of evolution. You might still reject it, but you wouldn't write so many of the seriously uniformed things you do.

Tom Mueller said...

@ Barb

I teach Biology in a Canadian backwater that is extremely big-C Conservative Christian. Sometimes, I think there are almost as many Baptist Churches as gas stations.

As a teacher, I am obliged to respect the belief systems of my students and never ever insult or belittle religious belief. As a matter of fact, I present myself as a church-goer (actually I prefer the synagogue) who taught catechism in the local parish when my own children were young.

OK – some of the local Baptists still look askance at my bona fides but moving on…

I spend more time than most teachers on taxonomy in general and Botany in particular. A quick “field trip” to a patch of meadow outside our classroom expansively illustrates Evolution in broad strokes. The commonalities of various algaes, one version of which possessed a common ancestor to mosses is no big jump. Followed by Club Mosses, followed by Ferns and transitional forms such as Ginkos leading to Conifers and Flowering Plants. My taxonomic survey in Botany is in fact quire more detailed, but again moving on…

Only with great effort do I manage to deflect any implication of a vector of progress to flowers and coated seeds and some presumptive Scalae Naturae”.

But “alea jact est” & beware the thin edge of the wedge!

Students have no trouble conceding the cogency of evolution in non-threatening botanical terms eventually leaving me with:

“Alright already, … I get it, but just don’t tell me I am descended from a Chimpanzee!”

“If Humans evolved from Chimpanzees, how come there are still Chimpanzees?”


Therein lies the rub… evolution is NOT a problem and can be easily conceded as cogent. Human Evolution – now there is the problem.

If shibboleths can be slain in Botanical terms, then moving on to animal and ultimately to primate evolution represents less of a challenge.

This thread has been inspirational and has caused me to consider a complete rethink of how to present Botany in evolutionary terms.


Larry Moran’s challenge

1 - I think it's important to teach biochemistry from an evolutionary perspective and it's important to teach students that there's more to life than just flowering plants and humans…
2 - The same strategy applies to teaching the rest of biochemistry from simple pathways to more complex pathways avoiding the impression that what we see in humans (e.g. glycolysis) is standard.


Part 1 – I was already doing. Part 2 – now there is a challenge I gratefully acknowledge that requires improvement.

I remain ever grateful to Otangelo Grasso

I can think of no better contradiction to Irreducible Complexity and Intelligent Design than Photo-Phosphorylation and its latter tag-on Photosynthesis which is all about PGAL (G3P) and not Glucose/carbohydrate metabolism. I will be using material gleaned from this thread in class.

Final Word to Larry Moran:

Thank you!

Bill Cole said...

lutesuite
One could ask Bill Cole for counter examples of successful predictions from intelligent design, but he has already attempted to head that off by conceding that ID is a hypothesis that cannot be used to make predictions. One has to wonder how something could be a hypothesis without generating predictions. And no, Bill, the problem does not magically disappear if you mislabel your "hypothesis" as an "inference."

The most solid advocate IMHO is Michael Behe and if listen to any of his lectures you will understand what the science is and is not. Intelligent design is not a tested scientific hypothesis it is an inference. Your stronger debating strategy is to attack its limitations and not try to create a strawman.

Tom Mueller said...

@ Bill Cole

Just to make sure we understand each other, I did in fact answer your question here:

http://tinyurl.com/hox9jtr

I do not want to accused of a typical creationist tactic of hiding from the original difficult question and later on moving goal-posts

Bill Cole said...

BW
"BC, you're right that the blood clotting example and the photosynthesis example would never convince a person of the truth of evolution unless that person already understood evolution. Without that deeper understanding, he'd never grasp what was wrong with the anti-evolution arguments. The problem here isn't circular arguments so much as self-reinforcing ignorance."

Thanks for understanding my point. When I say circular argument I simply mean assuming up front your conclusion. It is only effective when your audience accepts your assumption. I started on this subject 15 months ago and will continue trying to educate myself. I think the problem that I see with the theory is becoming recognized by many inside the field at this point. Can you give me in your own words the best case argument for common decent? Does it require a single tree to still be a valid theory? Does common decent imply a mechanism for change is understood?

Unknown said...
This comment has been removed by a blog administrator.
Anonymous said...

BC, I do have a life, you know, that extends beyond commenting on Sandwalk. But maybe I'll play for a while -- if you do your part.

Let's take this beyond mere words. Pick up a field guide to birds of North America. (Or some other group of animals, if you strongly prefer.) Make sure you get a guide that's intended to show you all the species in an extended area. You can borrow it from a library.

Sit down for a couple hours and leaf though the book. Compare different species, and see how they tend to fall into groups. Compare adult males, female, and juveniles. Ask yourself how the different species and groups differ. Look at details that often aren't well illustrated, like beaks and feet. In birds, think about whether there are three toes or four per foot, for example, and where the 4th toe is on the foot.

Come back tomorrow and tell me which book you examined carefully.

judmarc said...

Does it require a single tree to still be a valid theory?

Only in the minds of those who oppose it on no good scientific basis. We've known for a very long time (ever since HGT was discovered) that evolution can't literally be the explanatory "tree" metaphor. What is true, however, is the existence of nested hierarchies, first evidenced by morphology, then independently confirmed by genealogy. (Oh, by the way, there's yet another experimental prediction and confirmation of the truth of evolution for you.)

Bill Cole said...

BW
"BC, I do have a life, you know, that extends beyond commenting on Sandwalk. But maybe I'll play for a while -- if you do your part."

I will do this. Looking forward to your comments.

Faizal Ali said...

@ Bill Cole:

The most solid advocate IMHO is Michael Behe and if listen to any of his lectures you will understand what the science is and is not. Intelligent design is not a tested scientific hypothesis it is an inference. Your stronger debating strategy is to attack its limitations and not try to create a strawman.

Here is just one example, among many others I could have chosen, courtesy of one of ID's most noted proponents, where ID is explicitly described as a "hypothesis", not just an "inference":

http://www.evolutionnews.org/2011/03/a_closer_look_at_one_scientist045311.html

Can you give me any reason that I should take your word on the issue, as opposed to the people the Discovery Institute have specifically hired to explain ID to the public? Why should I believe your claim? Do you really expect me to believe that Behe has admitted to have written two books and many articles on an idea he believes is not supported by any scientific evidence?

That is not to say I even accept your distinction between a hypothesis and an "inference". If I find raccoon tracks around my garbage bin after it has been tipped over, I can infer from this that raccoons were responsible. And this inference will also allow me to predict that the next time it is knocked over, I will also find raccoon tracks.

Can I take from the fact that you have failed to respond to my post describing your contributions as intellectually dishonest and hypocritical, that you admit that this is true?

Bill Cole said...

Lutesuite
http://www.evolutionnews.org/2011/03/a_closer_look_at_one_scientist045311.html

"Can you give me any reason that I should take your word on the issue, as opposed to the people the Discovery Institute have specifically hired to explain ID to the public? Why should I believe your claim? Do you really expect me to believe that Behe has admitted to have written two books and many articles on an idea he believes is not supported by any scientific evidence?"

If you are getting your information solely from the Discovery Institute then it is understandable that you are confused by the science. I would take information from the NCSE and the Discovery Institute with a grain of salt. Larry has had many disputes with what Casey Luskin has claimed and I can't remember a time I did not agree with Larry. My description is based mostly on conversations with Michael Behe and that is the main source of my view of ID. I think Steven Meyer does a reasonable job of explaining the ID inference but he loses me when he says that it can make predictions. Based on my recent conversation with Behe, he is not confused on this issue.

Faizal Ali said...

@ Bill Cole:

So you're saying I should base my views on vaguely described conversations you claim to have had with Michael Behe, rather than what Behe and other ID creationists actually write? What a bizarre suggestion.

Although, I must say, it is tempting for me to believe that the ID creationists will secretly admit to the intellectual bankruptcy of their enterprise in private, off-the-record conversations, I will require a more credible source than yourself before I take this as fact.

Bill Cole said...

Lutesuite
Although, I must say, it is tempting for me to believe that the ID creationists will secretly admit to the intellectual bankruptcy of their enterprise in private, off-the-record conversations, I will require a more credible source than yourself before I take this as fact."

This is just my humble opinion. I agree with you and Larry that there is a lot of fluff coming out of political activist groups and thank both you guys for helping me sort it out. The question is when we peel off all the fluff is there any substance? I attended a web seminar Michael Behe presented and was able to converse with him. I think his position is solid, the question in my mind is what value does ID have?

Unknown said...

bwilson295-
If the universe is a creation of a conscious entity, then it is always reasonable to ask 'why' something is how it is.
Investigating how something happens may or may not be illuminating to any why answers.

Wouldn't it be more honest of you to say you don't know the answers to the 'why' questions then to say there are no answers?


Faizal Ali said...

If his position is as you describe it, and if it is solid, then that answers your last question: ID had no value.

Faizal Ali said...

No. It would be more honest to say that you don't know if the "why" questions even pertain.

Bill Cole said...

Tom
"If Bill Cole still persists in disagreeing, he must acknowledge that HE IS BURDENED with an anachronistic “WORLD VIEW” and that the burden of proof now rests with him to explain how:"

The statement that I objected to; it is a fact that we defended from fish. While I agree that you can make an inference argument from genetic and fossil record evidence, I cannot be convinced this is a fact at this point.If you have an argument that confirms this as a fact I am all ears.

Anonymous said...

JJ wrote, "If the universe is a creation of a conscious entity, then it is always reasonable to ask 'why' something is how it is." -- If, . . . then, this is true. However, if the universe isn't the creation of a conscious entity, then "why" is often a foolish question.

JJ wrote, "Wouldn't it be more honest of you to say you don't know the answers to the 'why' questions then to say there are no answers?" -- No. We have no evidence that the universe is the creation of a conscious entity, so assuming that the "why" questions have answers that we don't know yet is unjustified.

Tom Mueller said...

Bill Cole

You are resorting to transparent sophistry and my patience is wearing thin.

You are manipulating words on a page to score debating points when it is abundantly clear that you have already dismissed beforehand any plausibility to evolution, so what’s the point?!

Barb is correct to get on with her life and waste no more time on you and your ilk.

Here is my last attempt to indulge your silliness: Yes, in philosophical terms: of course evolution is not the only explanation possible. Perhaps Intelligent Design can be inferred.

Meanwhile, one could also argue that Newton’s Laws are not the ONLY explanations for the dynamics of the celestial spheres or the planets. Maybe the planets too are possessed of intelligence or are being pushed into elliptical orbits by angels. Maybe with some elaborate mathematical hocky-pokery, one can model the Earth as the Center of the Solar System. This too is still “possible” just as Intelligent Design in Biology is still possible.

Problem is, even though such supernatural premised explanations are POSSIBLE, nontheless they are not scientific.

What you fail to appreciate is that Gravity is BOTH fact and theory. Ditto Evolution.

Stephen Jay Gould, the greatest essayist on natural history must be whirling in his tomb as today’s confused debate on intelligent design persists! Like a repeatedly slain phoenix “Intelligent Design” raises from the discredited ashes of “Creationism” and like the mythical Hydra, two subtler sophists emerge for every beheaded casuist.

Over 20 years ago, Gould demonstrated that today’s reprise of an earlier debate is fraught with misunderstanding as laymen miscomprehend and misuse scientific vocabulary. http://www.stephenjaygould.org/library/gould_fact-and-theory.html

A scientific “theory” is not some admission of weakness conceding speculative status inferior to established fact. In scientific parlance, a “theory” is not “imperfect truth”. Theologians and epistemologists may debate “truth”, while scientists generate models of the universe called “theory”.

Just like Gravity and planetary motion, evolution is also fact! Again in scientific parlance, facts are data points, while theories are models to explain and predict data points. Thus gravity is both fact and theory. Apples persist in falling (indisputable facts) while scientists can debate how Einstein’s, Hawking’s or Barbour’s theories should sometimes (not always) supersede Newton’s theory of Gravity.

But even while the debate ensues, Newton's model still works when launching satellites into space - and Einstein's model still works when synchronizing those satellites' clocks with our slower clocks back on Earth (darned theory of relativity don’tchya know). Meanwhile, Hawking's and Barbour's equations go a long way to explain the cosmic dance of galaxies as observed from those orbiting satellites that were launched in simultaneous deference to two earlier theories.

Just like Gravity and planetary motion, so too Evolution is both fact and theory!

One may as well cite biblical exegesis suggesting the celestial firmament revolves around a stationary Earth, than deny the indisputable facts of evolution including the fact that that humans share a common ancestor with fish.

What still remains to be debated? Perhaps, how much of the inescapable fish/human common ancestor conclusion is to rely on Natural Selection as opposed to say Neutral Theory, or Nearly Neutral Theory.

I cannot be kind about this: your ravings belong to this site:

http://www.crank.net/science.html
.

Tom Mueller said...

@ Bill Cole

Just to make sure we understand each other, I did in fact continue my answer your question here:

http://tinyurl.com/z9bo8vu

Again, I do not want to accused of a typical creationist tactic of hiding from a difficult question and later on moving goal-posts by addressing a different question.

Bill Cole said...

Tom
"What still remains to be debated? Perhaps, how much of the inescapable fish/human common ancestor conclusion is to rely on Natural Selection as opposed to say Neutral Theory, or Nearly Neutral Theory."

This point I mostly agree with. Can we have a theory of common decent without a known mechanism? IMHO both neo darwinism and neutral theory are almost certainly wrong. I think the best answer is we don't know. This avoids layering science on top of faulty assumptions.

Tom Mueller said...

@ Bill Cole

Re: Can we have a (sic) theory of common decent without a (sic) known mechanism? IMHO both neo darwinism and neutral theory are almost certainly wrong. I think the best answer is we don't know. This avoids layering science on top of faulty assumptions.

How does one determine whether a
(sic) theory is correct or not?


Your deliberate obtuseness has crossed the line into hypocrisy and the only reason I am continuing this exchange is to set correct the public record and not allow your dissimilitude to poison the minds of impressionable naïfs

If X is a valid hypothesis (explanation), and one can perform Y methods (experiment), then one can predict Z as a specific measurable outcome.

When evidence from independent, and various unrelated sources all "converge" on the same conclusion, the empirical method has arrived at that sweet spot called “consilience” and the hypothesis is deemed “correct”!

That all said, scientific theory operates in operational context. Convenience and utility are also important criteria for scientific models, not just parsimony.

Engineers need not invoke Quantum theory to orbit a satellite within metres of its intended orbit, Newton’s far simpler equations are quite sufficient. However, Newton’s theory will not synchronize the satellite’s clocks and clocks remaining on Earth. Einstein’s more complicated theory will fill the breech. However, Einstein’s theories fall short when attempting to explain details of an expanding universe, rotating galaxies or dissipating Black Holes. That is where Barbour and Hawking’s equations need come into play.

How does one determine how a (sic) theory of gravity is correct or not?

They are ALL correct – you casuistic sophist - They are all correct when they confirm prediction in Popperian fashion, in context specific fashion!

Back to evolution as fact and theory.

Evolution is fact no less than gravity is fact. Evolution is theory no less than Gravity is theory. Can different theories of Evolution be simultaneously true? YES – no differently than different theories of Gravity can be simultaneously true?

Please cease and desist with your blatant intellectual dishonesty.

Tom Mueller said...

@ Bill Cole

Just to make sure we understand each other, yet again, I did in fact answer your disingenuous question here, you mendacious SOB!

http://tinyurl.com/h5pwxpr

I do not want to accused of a typical creationist tactic of hiding from the original difficult question and later on moving goal-posts.

That said - I am done with you!

Basta!

Tom Mueller said...

In simple English, simple enough for even Bob Cole to understand:

An assumption is NOT the same as a conclusion!

Countless scientists have commenced with the assumption of the bible being true

and

...despite all such prejudicial assumption; inevitably and inexorably arrived at the same conclusion: that the evolution is "correct" both as fact and as theory.

Admittedly there are some who do not. The vast majority are suffering some personality defect and really deserve no more attention. There are others who are simultaneously intelligent, earnest and do not. But they are operating at an epistemological level far beyond the grasp of the likes of Bob Cole.

I refuse to throw any more pearls before swine on this forum.

Bill said...

Thank you, everybody, for the entertainment (creationists) and insightful commentary (scientists). In my work supporting science education policy I find honing my rapier's wit on these "arguments" very useful. I scare-quote "arguments" because creationists *coughGrassocough* don't have arguments so much as unfounded assertions. Never the less, one can get tangled up in the Sargasso Sea of minutiae if not careful.

Thank you, Tom, for the great summary. It's a keeper.

Unknown said...

lutesuite-
The answer to ‘Do the why questions even pertain?’ will be ‘yes’ or ’no’ depending on one’s premise regarding if the universe is a creation or not among other things.

bwilson295-
We agree- if the universe is a creation, then why questions might make sense where if the universe is not a creation then the why question probably won’t make sense.
So if one thinks the universe is a creation, then it makes complete sense to assume any ‘why’ question unanswered is unanswered due to ignorance. It would be utterly illogical and ‘giving up’ and ‘motivated stopping’ to think otherwise.
Right?

Unknown said...

bwilson-
I'm sorry, but if you won't see the logic of the other, then I'm really afraid because I'm pretty sure it's going to be more difficult to get the other to see your logic.
Maybe I'm being a 'concern troll' or whatever that is about this topic.

Faizal Ali said...

The answer to ‘Do the why questions even pertain?’ will be ‘yes’ or ’no’ depending on one’s premise regarding if the universe is a creation or not among other things.

Exactly. The value of the question is no more than that of "What colour are the toe nails of the Loch Ness Monster?" Until one first demonstrates the Loch Ness Monster exists, why should anyone waste their time pondering such a question?

Tom Mueller said...

Hi Bill

Thank you for the compliment.

I need to clarify one last point. In a moment of indignant outrage, my contradiction of Bill Cole presented an apparent false dichotomy.


Countless scientists have commenced with the assumption of the bible being true

and

...despite all such prejudicial assumption; inevitably and inexorably arrived at the same conclusion: that the evolution is "correct" both as fact and as theory.


A disinterested outsider could conclude I presented a either/or scenario where the cogency of evolution rules out the "truth" of the Bible.

That was not my intent as I indicated later with my:

There are others who are simultaneously intelligent, earnest and do not [subscribe to evolutionary theory]. But they are operating at an epistemological level far beyond the grasp of the likes of Bob Cole.

Bottom Line: some of the IDiots present need some lessons in Biblical Hebrew. Talmudic sages have for centuries past understood that Genesis is not to be read literally. The pages of commentary on the very first word of Genesis establish that point.

In other words: a correct understanding of Biblical Hebrew leads to one inescapable conclusion. The Bible cannot and does not contradict Science.

But this forum presents neither the time nor the place to defend the cogency of NOMA.


Anonymous said...

Tom, Thanks for the advice on teaching about evolution to people who are resistant to it.

Anonymous said...

Exactly. "Why" questions don't make sense unless the universe is created by ac conscious entity. We have no evidence for such a being. Even more relevant, the "why" questions don't give us answers (unless asked in such a way that they're really "how" questions); this failure is evidence that "why" questions aren't relevant. Which suggests that there is no conscious creator-entity, at least in any form that is relevant to questions about the universe's history.

Bill Cole said...

Tom
"Evolution is fact no less than gravity is fact. Evolution is theory no less than Gravity is theory. Can different theories of Evolution be simultaneously true? YES – no differently than different theories of Gravity can be simultaneously true? "

Gravitational effects can be repeatably measured. Show me an example
of how you can measure or model how specie a evolves into specie b using RMNS or neutral theory?

Faizal Ali said...

The Bible cannot and does not contradict Science.

Well, sure. Neither does creationism, if not read literally. So exactly what is the significance of your statement?

Joe G said...

Thank you Larry for proving that there isn't any way to test the claims of your position. You are a legend in your own little-bitty mind. Too bad I no longer go to Toronto to work at OPG or I would pay you a visit and shut you up.

nmanning said...

Eric writes:

"What do you know besides your ideology?

I have 100 questions for you to prove your beliefs. If you provide scientific or reasonable evidence for 1o of those questions, you can pass.

Are you interested?"


Most ironic - I could ask the exact same of you. I have, in fact, asked many ID advocates/creationmists for the actual supporting evidence FOR their claims over the course of more than 20 years. And each and every time, without exception, all I have ever received were complaints about evolution. 'Evolution cannot explain X!' 'Darwin was a drug addict!' 'Darwin=Hitler!' 'Dembski's math proves Jesus!' etc.

But never, ever any actual evidence that SUPPORTS the alternative "theories" put forth by religious zealots and anti-science advocates.

I'm thinking that your implicit hubris would wither and die were you put under the same spotlight.

nmanning said...

"Evolutionary novelties through mutations, migration, genetic drift, and natural selection is a prediction that HAS BEEN FALSIFIED through the good work of dedicated scientists,"



Where are the copy-pasted article titles that support this?
When will you pull a Gish-Gallop-style, Woodmorappe-citation bomb to "prove" your unsupported assertion?

Unknown said...

Google: Where Do Complex Organisms Come From? The second link will direct you to the topic at my library. If you scroll down the first post, there is a series of links to mainstream scientific papers, which will point out a series of mechanisms that define body form, that have nothing to do with genetics, but epigenetics, various epigenetic codes, and even " Junk DNA". I am more than happy to debate this stuff at FB. Not here.

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