Sunday, November 09, 2008

Science Discovers God – Again


[history of the universe]

In the most recent issue of Discover magazine, (12/2008) there is a remarkable article “A Universe Built for Us” (page 52 to 58). This article discusses the strong antropic principle. This is the discovery that physical laws have apparently been fine tuned to allow life to exist. One additional confirmation seems to be the discovery of dark energy during the past ten years. According to Leonard Susskind, if there would be more dark energy, stars would never have formed. Steven Weinberg states “This is the one fine tuning that seems to be extreme, far beyond what you could imagine just having to accept as a mere accident.”

So there you have it –science proves that God created the universe. And this not the first time in recent years science has confirmed religion. The discovery of the complexity of DNA makes an accidental origin of life even more absurd. (Some scientists have been forced to speculate that aliens planted life on earth, although there is no evidence of the existence of such aliens.) The discovery of the Big Bang proved that the universe is not infinitely old but had a creation – and therefore apparently a transcendent Creator.

Skeptics suggest that perhaps there are an enormous number of universes, not merely one, and therefore simply by blind chance one would be hospitable to life. According to Bernard Carr “If you don’t want God, you better have a multiverse”. There is however a problem. There is currently no evidence of other universes. There is however evidence of God.

People who are addicted to a selfish, debauched way of life will never be convinced of Torah. Their overwhelming denial will overcome any objection. As an example of this type of thinking, witness this young woman (view from 4:00) . She is 24 years old, addicted to methamphetamine and alcohol and supports herself as a stripper. Her family is desperate to save her life. She adamantly claims that she is happy and refuses to change. Nothing can be said to reason with certain people.

Those of us, however, who are rational and sober, can enjoy and be excited by the unfolding discoveries of science and the miracles which it continues to reveal.

71 comments:

Crawling Axe said...

A few questions.

1. What is our measure whether something is accidental or not? Do we not measure it by comparing to nature (otherwise, how do you calculate something as being accidental or too improbable to be accidental — where is the frame of reference)? So then how can we turn around as say that nature is not accidental?

2. How does the scientific evidence point towards specifically Jewish G-d (not vs. other religions, but vs. deism, for example)?

3. What is evidence of Jewish G-d from Jewish tradition lacking without scientific evidence?

jewish philosopher said...

Something demonstrating complexity and purposefulness must have been designed rather than occuring spontaneously.

Nature and Jewish tradition support each other. Nature demonstrates a designer. Tradition tells us Who that designer was.

The Raz said...

Interesting but why not be transparent and offer your readers the article from the previous month entitled "Science's Alternative to an Intelligent Creator: the Multiverse Theory" from the same publication.

http://discovermagazine.com/2008/dec/10-sciences-alternative-to-an-intelligent-creator/article_view?b_start:int=0&-C=

Present your readers with all the information and you will have a better discussion.

Personally, I love this subject. You should tackle it more albeit you should be more willing to put all the cards on the table.

P.S.- You didn't do a good job jumping from multiverse to drug addict. I don't know where that leap came from but I think a tie in paragraph would have helped your argument.

jewish philosopher said...

I mentioned the multiverse idea.

The Raz said...

You skimmed over it and neglected to mention a counter argument within the same publication.

Moving on, I have real question and being that you have a greater halachic background then myself (yes even I think that sounded sarcastic coming from me), can you think of a plausible way of allowing a mutliverse theory i.e. string theory that would coalesce with Jewish ideas of the Universe.

I'm interested to hear if you have a take on it and really hope you do not dismiss the "possibility" with a 1-2 sentence response. So ponder it for a bit and get back with me on it. I know the answer isn't really a short one so I don't expect a response in a few minutes.

jewish philosopher said...

Which counterargument didn't I mention?

Jews do believe in other universes. For example, there is a world of angels.

The Raz said...

"Jews do believe in other universes. For example, there is a world of angels."

So you’re proposing that "if" other universes existed they may be the realm in which celestial beings existed. My expansion of that would be one maybe a plane in which a angels exist, one for souls (maybe differing planes some closer to Hashem some further), possibly even some representing the Kabalistic levels of keter, chachma, bina etc. Am I on the right track there? It’s an interesting idea.

Anonymous said...

One problem I have with multiverse is that it doesn't answer all the questions. Multiverse explains why the laws of our universe are the ay they are. We just happen to live in the one were all the laws are exquisitly fine-tuned to accomodate life. But there are other anthropic coincidences that are facts about our universe that are the result of the applicaton of the laws. For example the amount of mass in the universe is just right. The laws of physics don't require that the universal mass be exactly what it is. Also, the number of protons and electrons is roughly the same. There is no reason why this should be the case, but it is. And why is the universe all matter and not antimatter? In every experiment performed on Earth, wehnever a particle of matter is produced a corresponding particle of antimatter is produced. But not in the Early universe.

Crawling Axe said...

Something demonstrating complexity and purposefulness must have been designed rather than occuring spontaneously.

What are your criteria for complexity and purposefulness?

A puddle is sitting in a hole in the ground, whose form is exactly the same as that of the puddle. Is it the case that this hole was designed purposefully for the puddle, since it fits its shape perfectly?

If I am driving in White Mountains in New Hampshire and see a mountain peak that looks very much like a bear, is this proof that it was designed by someone?

jewish philosopher said...

A complex mechanism with many parts all working efficiently for a certain purpose.

Crawling Axe said...

Multiverse explains why the laws of our universe are the ay they are. We just happen to live in the one were all the laws are exquisitly fine-tuned to accomodate life. But there are other anthropic coincidences that are facts about our universe that are the result of the applicaton of the laws. For example the amount of mass in the universe is just right. The laws of physics don't require that the universal mass be exactly what it is. Also, the number of protons and electrons is roughly the same. There is no reason why this should be the case, but it is. And why is the universe all matter and not antimatter? In every experiment performed on Earth, wehnever a particle of matter is produced a corresponding particle of antimatter is produced. But not in the Early universe.

All soap bubbles are approcimately spherical. Why is that the case? Isn’t it amazing that every single soap bubble is of the same shape? I mean, out of all the possible shapes in the world, bubble “choose” only round ones — never a pyramid, an elephant head, or a star?! What’s up with that? Statistically, it just doesn’t make sense — somebody must be controlling the bubbles’ shape.

The answer, of course, is that only the round shape is stable. Whenever a soap bubble starts tending towards some other shape, it bursts. As a result, the spherical soap bubble are the only ones we see around.

People ask: isn’t it a coincidence that life happened where there were conditions perfect for it to happen? No more a coincidence than whenever you’re in a mall, and there is a diagram with an arrow that says “You’re here ↓”, you happen to be exactly there. Obviously life was able to exist only in the conditions which allowed for its existence.

jewish philosopher said...

Frankly, I am not an expert on all the physics involved. However, what physicists seem to be saying, and I understand to some extent, is that the universe is more than merely symmetrical. They seem to be saying that the universe is a complex environment with many factors fine tuned to make life possible - a life supporting machine in other words. Machines, in the sense of a complex mechanism with many parts all working efficiently for a certain purpose, require an intelligent designer.

Rich Perkins said...

Does any of this really prove God?

It just shows that we as humans don't know the answer to everything. That there are things that, with or without God, we may never understand.

You are taking this plus the Torah and saying that since we don't know and since Judaism offers an explanation, it must be true.

You may be right that God created the universe, but having science say they don't know is hardly a proof for His existence.

Pen Tivokeish said...

There was a time when we didn't know that DNA exists. Come along Watson and Crick and show us DNA.

If I was a creationist at that time, I would be willing to bet my bottom dollar that the DNA sequence present in each kind will show that each kind was created individually and is not a member of Darwin's tree of life, thus refuting evolution.

Well, it was not to be. The DNA sequence confirmed the Evolutionist's tree of life.

So for you to use DNA as proof against evolution is beyond contempt.

Crawling Axe said...

Universe is also a fine-tuned machine for existence of gravity. A bubble is a fine-tuned machine for existence of round shape. A puddle-hole is fine-tuned to match the shape of the puddle (the water). Phenomena that we see are results of the conditions that created them — obviously, such conditions are fine-tuned for these phenomena to exist.

A complex mechanism with many parts all working efficiently for a certain purpose.

Yet, a theory explaining how complex mechanisms can arise out of chaos already exists: Theory of Evolution. It states that through energy of the system flowing towards more stable mechanisms constantly adopting to changing environment, development of complexity can happen. No Grand Designer is necessary.

(Do you think snowflakes are a proof of G-d’s existence? They look complex enough for me. Yet, their shape can be explained by water molecules combining in least energy-consuming formations.)

Or Theory of Economics, which states that through money flowing to entrepreneurs who satisfy the needs of the market the most, progress and development of civilization can happen. No Grand Governor is necessary.

I am not saying it it a successful proof of atheism; I am just saying that argument from design is not a good proof of Hashem’s existence in my opinion.

Anonymous said...

There are at least sixty different parameters that are ballnced just so. Every single law of physics is balaned just right. Evey any one was of by a slight amount, then the universe wouldn't exist, or would ahve exapnded to fast for satsr to form, or consist entirely of hydrogen or entirely of helium. Life would be impossible. Now, even with all this fine tuning, we still couldn't predict the existanse of life from the universe as it is. It is really, extemely unlikely, even with all the anthropic conditions just so, that simple molecules could come together and form a cell. Its like a factory for making microchips. The conditions have to be controlled very precisely or the manufacture of chips would be impossible. But even with all this precision, the chips cna't make themselves.

Anonymous said...

Adn there is a great deal of controversy about the "tree of life." For example, we don't know if we are more closley relaterrd to crusataceans or mollusks.

And if DNA is the blueprint for life, I would expect similar organisms to have blueprints that are closer than dissimilar organisms. A car has more oin common with a truck than it does with an airplane. I would expect the designs for a car to have more in common with a trucks designs thaan with an airplanes designs. This doesn't mean that the car evolved from the truck.

jewish philosopher said...

"Does any of this really prove God?"

It proves that the universe is a machine and a machine must have a designer. The Torah tells us who he is.

"If I was a creationist at that time, I would be willing to bet my bottom dollar that the DNA sequence present in each kind will show that each kind was created individually and is not a member of Darwin's tree of life, thus refuting evolution."

I'd bet my bottom dollar DNA would be similar for all life since all had one creator.

"Yet, a theory explaining how complex mechanisms can arise out of chaos already exists: Theory of Evolution"

Which I have proven false.

For the universe to have arisen by chance is like speculating that a hospital incubator arose by chance.

Crawling Axe said...

All the “disproofs” of Evolution are similar to Bible Criticism. They don’t really understand fully what they are disproving, all the arguments have been answered in many places, and so on.

But, if this will lead more people to have emunah, fine. Yasher koach.

A car has more oin common with a truck than it does with an airplane. I would expect the designs for a car to have more in common with a trucks designs thaan with an airplanes designs. This doesn't mean that the car evolved from the truck.

No, it doesn’t. But first of all, the fact that some complex things were designed means that it is possible for complex things to be created by a designed. Nobody ever argued with this. Theory of evolution simply shows the lechoira, it is possible for complex things to arise through laws of the Universe. Also, cars or trucks don’t reproduce. Living organisms do. Living organisms have variations. Living organisms change — and the most successful of them survive. All of these things are facts. Everything that follows is logic.

Now, one could argue with existing particular aspects of the theory, one can say that there are aspects of the evidence that need to be explained, but overall, theory makes sense and is consistent with existing evidence.

This in itself does not prove atheist point of view. Theory of Evolution does not contradict existence of G-d. Nor does TE contradict Torah, in its most literal interpretation (6 days of creation, 5769 years ago, all events described literally and really happening). What it does contradict is assertion (without any further evidence) that complexity necessarily means an intelligent designer. This argument is just a bad argument. Many other numerous arguments and proofs are not.

jewish philosopher said...

"All the “disproofs” of Evolution are similar to Bible Criticism. They don’t really understand fully what they are disproving, all the arguments have been answered in many places, and so on."

My questions have never been answered.

Anonymous said...

One more problem with the multiverse theory. There is no reason why the universes have to be different. They could just as easily be all the same, with the various anthropomorohic parameters making life impossible. So it ultimatly doesn't answer the question.

Crawling Axe said...

My questions have never been answered.

Like what? Why don’t we see a collection of fossils bringing evidence to smooth transition from one species to another? Imagine you are on a car trip from NYC to LA. Once in a while your son sitting in the back seat takes a snapshot — not at anything necessarily interesting, just at random. Sometimes a few snapshots of the same place, sometimes only one.

When you arrive to LA, you present your son’s documentary of your journey across US. When people look at it, they ask: “Why isn’t there a smooth transition from place to place? All you have is some random shots.” Your answer, of course, is that this is not a movie. Snapshots of some places were taken at random, and there is no reason why you should see every single yard documented — so, of course, you won’t have smooth transition between places.

What’s another question: why is there sudden explosion of diversity or complexity after every catastrophy? Why, after some dictatorial government collapses, there is suddenly a wide range of groups trying to control the country, each with its own philosophy, tactics, leaders, membership demographics, etc.? Because before there was a monopoly on power, where only a few parties existed successfully directing all the resources towards themselves. Then — revolution, and a vacuum of power created possibility for all different group to spring up and grab their share of resources. Eventually, it comes down again to only a few groups having control of the country (each in their own niche), but at first we always observe an explosion of diversity. The important detail that your question ignores is that a catastrophy does not wipe out all complex life down to bacteria — it wipes out a bunch of species which were dominating their ecological niches, were very-very slowly evolving and did not allow other species to evolve. Like dinosaurs and mammals. When dinosaurs were wiped out, mammals (who were a few rodents at the time) were free to explode in all possible variations, trying to adapt to environment the best way — so there was stimulus (so to speak) for increasing complexity and diversity.

All the other questions are similarly answered in many standard textbooks, articles, online sources, etc., etc. The problem is: proponents of ID theory read Boehe’s books but don’t read articles refuting them and showing how his books make no sense from the point of view of molecular biology. One such guy told me his excuse: “Well, I am not an expert in molecular biology...” But expert enough to understand and agree with Boehe’s books. Exactly the argument of Biblical critics: I don’t know Loshen Koidesh, I don’t know Arameic, I am not an expert in Talmud, in Hebrew grammar, in Chumash, in logic, but what Biblical criticism tells me just makes sense.

jewish philosopher said...

According to you, we should welcome a nuclear holocaust or at least global warming. A major catastrophe just makes way for progress. I wonder why most people don't realize that.

Anonymous said...

"proponents of ID theory read Boehe’s books but don’t read articles refuting them and showing how his books make no sense from the point of view of molecular biology. One such guy told me his excuse: “Well, I am not an expert in molecular biology...”"

I'm not an expert in molecular biology, but I've read articles refuting Behe's books. And IMHO, they don't succeed. They, at best make the problems a little easier.

Crawling Axe said...

Well, nobody said that it was good for dinosaurs when the catastrophe happened. If a nuclear holocaust happens, chv”sh, there will probably be a proliferation of species and increase in complexity of already existing species. Doesn’t mean we will fare well.

Another example: removal of Sanhedrin authority from Jewish population led to great diversification of views, as Rambam states, but we don’t believe this was a good thing subjectively. (The same thing with removal of rabbinic authority from Jewish masses leading to appearance and flourishing of apikorsis like Reform, Conservative and Modern Orthodox movements).

Regarding global warming: most famous ancient civilizations prospered in a climate about couple degrees warmer than the one today. On the other hand, side effects of global warming might be worse for enough people for us to care (not that I believe we can stop global warming by not driving in SUVs — which may, however, be a good idea on its own).

Crawling Axe said...

One more problem with the multiverse theory. There is no reason why the universes have to be different. They could just as easily be all the same, with the various anthropomorohic parameters making life impossible. So it ultimatly doesn't answer the question.

That’s not a problem. By definition, there could be no confines that directed the First Cause to create a particular Universe (otherwise it wouldn’t first cause). So, our particular Universe sprung out of the First Cause with no particular reason for its particular “form” (i.e., its particular laws of physics, specific properties of matter, etc.). Any other Universe that theoretically sprung out of the First Cause did not have in any way to look like ours — in fact, it would be bizarre if it did (it would mean that something is affecting the specific form of the Universes that the First Cause produces, which would go against definition of a first cause).

Neither would the First Cause be confined to producing only one Universe — in essence, we cannot say that the First Cause could be confined in any way at all.

So, it actually makes more sense (unless additional information tells us otherwise) that the First Cause produced more than one Universe (possible, infinite number) with very diverse properties. In some of the Universes, laws lead to just empty boring Universe which could not sustain life. Why aren’t we in that Universe? I think it’s obvious — because it couldn’t sustain life. Other Universes — like ours — could sustain life, but things just didn’t turn out the right way, and life did not happen. In some, however, it did. Voilá.

I am not saying I believe in this — we have evidence that this is not the cause, but if you don’t know anything about this evidence (revelation of the First Cause at Mt. Sinai to a full nation), the above explanation does seem plausible — at least theoretically (obviously, unless we have evidence, we cannot call that explanation scientific, just philosophical).

jewish philosopher said...

"If a nuclear holocaust happens, chv”sh, there will probably be a proliferation of species and increase in complexity of already existing species. Doesn’t mean we will fare well."

A nuclear would mean a decrease in complexity. Larger animals and plants would become exinct and the world would return to insects and shellfish.

The problem with the fossil evidence is not merely that it does not demonstrate evolution. It demonstrates something different - catastrophism. All the desperate apologetics don't change that.

Crawling Axe said...

A nuclear would mean a decrease in complexity. Larger animals and plants would become exinct and the world would return to insects and shellfish.

Well, it depends how large a nuclear explosion would be. But even if to such a degree as you described, still, an immediately following explosion of speciation and diversification would happen.

Besides the problem of some individual questions not being good questions, there is a deeper problem. You think that just because you can show a bunch of problems with a theory, a lot of counter-evidence, and even internal inconsistencies, the theory must be false or rejected by logic. That's not true at all -- or at least, not always true. It is true when evidence and arguments against some theory overwhelms evidence and arguments for it. It is not true when relatively, evidence against is much smaller than evidence for.

In the practice of science, we have accepted theories which had major problems and inconsistencies (e.g., Ptolomey's model of the solar system; Newton's theory of gravitation; quantum mechanics, view of finite Universe, view of infinite Universe, and so on), yet were successful overall in explaining what they had to explain and did not have better alternatives. People just hoped that these problems were secondary and marginal and would eventually be explained by more facts, details or arguments without changing the essence of theories (and if the essence of theories had to be changed, so be it, but until we see this as necessary...).

Furthermore, there were paradoxes in everyday life which we agreed were paradoxes but continued to go on living. For instance, Xeno's paradoxes which "proved" (lechoira) that motion is impossible. Everybody agreed they were valid paradoxes, but nobody thought for a second that motion was impossible. It took 2300 years until the advent of Calculus to figure out how to solve these paradoxes, yet people were not too disturbed all this time.

Another example is free will. We still have not solved the stoics' paradox about free will (free will cannot lead to accountability, because if it obeys rules --- internal or external --- the person cannot be accountable for rules he did not set; if it obeys no rules and is, therefore, random, a person should not be responsible for randomness generator inside his head; yet, if we do not consider accountability and free will, any decision becomes meaningless --- just like with Xeno's paradoxes, no action is possible). At the same time, we are living our lives and having normal society and religion.

In Torah there are many contradictions, problems, unanswered questions and so on. Talmud has a saying: a kasha (question about Talmudic logic) has never killed anybody. Yes, there is a problem, yes it is unanswered, yes we need to look for ways to answer it, but overall, our system works well in explaining what it needs to explain, and we will work hard to iy"H explain the problem at some point.

Theory of Evolution has a great explanatory power about many phenomena. Many aspects of fossil record, phylogenetic tree, genetics, and so on are consistent with TE. I would say most of the aspects are. There are, admittedly, problems, questions and inconsistencies, some of which are those that opponents of TE constantly cite --- but these in themselves do not disprove TE, anymore than an unanswered inconsistencies between quantum mechanics and theory of relativity disprove either (I was going to give an example with Talmud, but decided not to compare such things). Opponents of TE cite examples of problems with TE, without citing also facts that support TE, and to an unsuspecting reader, it seems that indeed, the whole theory is ludicrous, that no self-respecting scientist could believe that, and that they were probably brainwashed, or there is some liberal conspiracy going on. The truth is far from this. (Now, in economics, on the other hand, there is a lot of brainwashing and liberal conspiracy happening --- but economics, unlike biology, does not have strong scientific background or community, so such things easily pass.)

The same exact things that can be said about Evolution can also be said about, lehavdil, Judaism. Almost word for word. And opponents of Orthodox Judaism use the same tactics and arguments as opponents of Theory of Evolution.

Does this mean a Jew should believe in TE? No, he should believe that the world sure as a hell looks consistent with TE (and statement that the world is billions of years old), but since we have a better source (revelation of G-d at Sinai) which also explains why the world would look old and be young, why species would look evolved while they were created, we should believe the Jewish version of events.

Believing Judaism does not mean we ignore what reality tells us. We admit that reality says X, that Judaism says Y, that Judaism is right and that reality is an illusion created by Eibeshter. Or, perhaps, that X is an echo of some spiritual process, which made an imprint on reality, while Y is what really happened physically. No problem.

jewish philosopher said...

I readily admit that there are questions about Torah that I cannot answer. However, I maintain that the preponderance of evidence favors Torah.

In regards to evolution, there is simply no evidence favoring it. Genetics and taxonomy are not in any way based on evolution. Theoretically, the most fundamentalist Creationist could be a good geneticist or taxonomist. In fact, Carl Linnaeus, founder of modern taxonomy, and Gregor Mendel, founder of modern genetics, were both creationists.

Evolution is not a conspiracy. It is a false belief. People have deluded themselves to believe in evolution because doing so permits them to lead lives of selfishness and pleasure seeking with the belief that “God didn’t create me; evolution did.”

The Raz said...

I have enjoyed the crawling axe VS Jacob Stein debate (thanks JP for not censoring him) but both of you bring up some very good and weak points. If you listened to each other and didn’t brush off the others arguments you may come out with a deeper understanding of life. Your fight reminds me of Einstein’s rejection of Quantum Mechanics. He was so wound up in his own theories that he neglected to see the benefits of the other side. We still don’t have one unified answer but attacking a problem from all valid directions will help us pinpoint the essence, the answer we are seeking.
Are there holes in evolution? Yes and as time goes on we keep filling those gaps. Are there holes in the Torah? Yes and ignoring them will only exacerbate the problem. Acknowledge the short comings, embrace the differences and work toward the common goal. Torah and science can co-exist; Darwinian evolution and Torah can co-exist. It can be done even if that means altering both sides’ perspectives. From a religious standpoint, reassessing the Torah’s purpose and composition something alluded to by Rav Soloveitchik, see his brilliant reanalysis of Adam and Eve in The lonely man of faith.

The other option is to stay stubborn and risk another “earth being the center of the universe” fiasco we endured in Galileo’s time. Only now we have mass media and that kind of mistake makes organized religion look more antiquated then ever. The rejection of science by religion drives educated minds away from Judaism. Look to Hillel’s students for inspiration. They endured a plague because they stopped listening to each other, something that is clearly happening in this comment form.

Anonymous said...

IMHO the evidence for evolution is spotty at best, but the problems are huge. There are a million species that exist today, maybe even more. There are milloons more extinct species. If evolution is true, then there has been a lot of it happening. I would expect o see alot more evidence, not just a dozen or so "transitional series", or "possible natient species". On the other hand, so many processes at the biochemical level is extremely complex. They consist of numerous protriens or enzymes that must work together, either by bonding, or in sequence, or both. Each enzyme consists of hundreds or even thousands of amino acids that must be arrainged in a precise sequence. Then they must fodl into a very complex shape, exactly the right way. How can all these layers of complexity be the result of any sort of random process.

jewish philosopher said...

Our greater knowledge of genetics and paleontology makes evolution even harder to defend today than it was in 1859. And I don't believe that Torah and evolution can be honestly reconciled. The Torah said that man was created from the dust of the ground. Evolution says man was created from some as yet unidentified primate ancestor.

Crawling Axe said...

In regards to evolution, there is simply no evidence favoring it. Genetics and taxonomy are not in any way based on evolution.

Who said they were based on evolution? There is support to evolution to be found amongst them.

I don’t care who Gregor Mendel, Albert Einstein, Winston Churchill or Sir Arthur Conan Doyle were. I care about their ideas. Not their motivation for their ideas — just ideas themselves.

People have deluded themselves to believe in evolution because doing so permits them to lead lives of selfishness and pleasure seeking with the belief that “God didn’t create me; evolution did.”

Well, I am a really bad example for that. I know that G-d created me (and the world), know why, know how to achieve that goal and am trying to focus all my life on it. I really don’t have any personal emotional or even professional motivation to believe in evolution.

The whole practice of name-calling ad huminem arguments stating the “real reasons” why people hold certain views reminds me of an argument that people who are repulsed by homosexuality are latent homosexuals themselves. Following the same logic, homosexuals are latent heterosexuals? Believers in evolution are self-centered and promiscuous hedonists. And believers in G-d, by the same token, are driven by their insecurity, personal sexual repression, fear of death and lack of self-esteem and self-reliance? What exactly does name calling achieve?

And even if the above was true in some cases — so what? What do we care what motivation somebody had behind his ideas? We should judge ideas for what they are, their face value, not motivation behind formulation of them.

I have enjoyed the crawling axe VS Jacob Stein debate (thanks JP for not censoring him) but both of you bring up some very good and weak points. If you listened to each other and didn’t brush off the others arguments you may come out with a deeper understanding of life. Your fight reminds me of Einstein’s rejection of Quantum Mechanics. He was so wound up in his own theories that he neglected to see the benefits of the other side. We still don’t have one unified answer but attacking a problem from all valid directions will help us pinpoint the essence, the answer we are seeking.
Are there holes in evolution? Yes and as time goes on we keep filling those gaps. Are there holes in the Torah? Yes and ignoring them will only exacerbate the problem. Acknowledge the short comings, embrace the differences and work toward the common goal. Torah and science can co-exist; Darwinian evolution and Torah can co-exist.


Dude, I said exactly the same thing.

It can be done even if that means altering both sides’ perspectives. From a religious standpoint, reassessing the Torah’s purpose and composition

... is something which should not be done. We should not allow science to dictate to us how to view Will and Wisdom of G-d. Nor is this necessary. See Lubavitcher Rebbe’s letter on how science and Torah cannot contradict each other in principle, because Torah is infinite, perfect and true, while science is simply our best current version of what reality tells us.

On the other hand, so many processes at the biochemical level is extremely complex. They consist of numerous protriens or enzymes that must work together, either by bonding, or in sequence, or both. Each enzyme consists of hundreds or even thousands of amino acids that must be arrainged in a precise sequence. Then they must fodl into a very complex shape, exactly the right way. How can all these layers of complexity be the result of any sort of random process.

As I said, ignorance is not the best source for formulation of any ideas. Questions about biochemistry, irreducible complexity, Boehe’s problems with bacteria’s flagella, evolution of immune system and so on have been answered.

The Torah said that man was created from the dust of the ground. Evolution says man was created from some as yet unidentified primate ancestor.

Theory of Evolution tells you this is what it looks like. It is easily reconciled with an idea that Hashem created a human being in a particular form from dust (whatever that means), while the form itself evolved (in the mind of Hashem, kivyachol) from other forms. Or that Hashem created human form that looks like it descended from other forms. After all, many “rituals” in Judaism look like they descended from already existing rituals (bris, tzitzis, tefillin, writing on scrolls, wearing kippah, esrog and lulav, mikveh, etc.), yet these rituals are no less holy, because Hashem’s Will chose them as vehicles for fulfilling mitzvos.

jewish philosopher said...

"Well, I am a really bad example for that. I know that G-d created me"

Then you are a Useful Idiot.

"The whole practice of name-calling ad huminem arguments stating the “real reasons” why people hold certain views reminds me of an argument that people who are repulsed by homosexuality are latent homosexuals themselves. Following the same logic, homosexuals are latent heterosexuals? Believers in evolution are self-centered and promiscuous hedonists. And believers in G-d, by the same token, are driven by their insecurity, personal sexual repression, fear of death and lack of self-esteem and self-reliance? What exactly does name calling achieve?"

What about people who are for example Holocaust Deniers? These are millions of people, many of them educated, who believe in something ludicrous. Would it be wrong for me to suggest that they are doing so because of some unsavory ulterior motive, or must I accept at face value that they are convinced by the evidence and indeed they may have some good points?

Anonymous said...

"On the other hand, so many processes at the biochemical level is extremely complex. They consist of numerous protriens or enzymes that must work together, either by bonding, or in sequence, or both. Each enzyme consists of hundreds or even thousands of amino acids that must be arrainged in a precise sequence. Then they must fodl into a very complex shape, exactly the right way. How can all these layers of complexity be the result of any sort of random process.

As I said, ignorance is not the best source for formulation of any ideas. Questions about biochemistry, irreducible complexity, Boehe’s problems with bacteria’s flagella, evolution of immune system and so on have been answered."

I don't like the answers. For example the answer given to explain the flagellete is that the thirty or so proteins in the flagellet are the result of simultanious mutations in the five proteins in the bacterial toxin shooter, along with twenty five other mutations happening in other proteins all at once. Or you had the thirty mutations (its probably more like hundreds) happening over a period of time. Then you have cells producing all kinds of useless proteins untill all the right mutations happen ,a dn things fall into place. Can you see why I don't like it?

Crawling Axe said...

What about people who are for example Holocaust Deniers? These are millions of people, many of them educated, who believe in something ludicrous. Would it be wrong for me to suggest that they are doing so because of some unsavory ulterior motive, or must I accept at face value that they are convinced by the evidence and indeed they may have some good points?
Some of them may have ulterior motives, some are idiots and some are ignorant. The bottom line is: who cares? We should take their ideas and examine if they are true or not.

Then you are a Useful Idiot.
Somehow I didn’t have any doubt that you would point name-calling at me. Very mature. And a great kiddush Hashem too.

By the way, in your definition of a useful idiot is someone who trusts scientists. I don’t trust anybody in anything. I have enough education to be able to figure it out by myself.

I see, by the way, that you posted “Critique of 29 Evidences of Macroevolution”, but you didn’t post response to it by the author of “Evidences”.

I don't like the answers. For example the answer given to explain the flagellete is that the thirty or so proteins in the flagellet are the result of simultanious mutations in the five proteins in the bacterial toxin shooter, along with twenty five other mutations happening in other proteins all at once. Or you had the thirty mutations (its probably more like hundreds) happening over a period of time. Then you have cells producing all kinds of useless proteins untill all the right mutations happen ,a dn things fall into place. Can you see why I don't like it?

What? That’s not what the “answers” say. Read this.

DrJ said...

I am really out of your guys' league. But let me state very simply:
1. to refute Argument by design: A lake's shape and structure is very complex and has an evident purpose--to hold the water and life within it. Yet no designer was necessary.
2. To refute that the Torah offers an answer to cosmological and biological questions: The hare does not "chew its cud", nor does rain originate from the "rakiah" (heavens), nor could there be day and night before the sun and moon were "created".
3. The "biblical" God "broke" many of his "promises"-- like the eternity of kingdom of David (which is why the prophets and rabbis had to invent the Messiah and world to come), like the promise to Abraham, Jacob and Isaac that their seed would be "as numerous as the stars in the heaven" (which is why the rabbis had to invent reasons why Jews were being destroyed each time). Instead, the "biblical" God's people, for most of history, are weak, defenseless, numerically minute, and irrelevant to most of earth's humanity. Kind of a poor performace for an all powerful, jealous and glorious god.

jewish philosopher said...

Actually, a little while ago, I did correspond directly with Dr Theobald and he also was unable to answer my questions.

jewish philosopher said...

"to refute Argument by design"

The argument from design means that a machine, like a watch, must have a designer. A lake is not a machine.

"The hare does not "chew its cud","

I have a post about that.

"nor does rain originate from the "rakiah" (heavens)"

It comes from the ground where you live?

"nor could there be day and night before the sun and moon were "created""

Before the sun was created, there was time.

"like the eternity of kingdom of David"

David was promised by Nathan II Samuel 7:16 that "your throne will be established forever" which will be fulfilled in the Messianic era.

"like the promise to Abraham, Jacob and Isaac that their seed would be "as numerous as the stars in the heaven""

About 9110 stars are visible to the naked eye.

Anonymous said...

"I don't like the answers. For example the answer given to explain the flagellete is that the thirty or so proteins in the flagellet are the result of simultanious mutations in the five proteins in the bacterial toxin shooter, along with twenty five other mutations happening in other proteins all at once. Or you had the thirty mutations (its probably more like hundreds) happening over a period of time. Then you have cells producing all kinds of useless proteins untill all the right mutations happen ,a dn things fall into place. Can you see why I don't like it?

What? That’s not what the “answers” say. Read this."

You're right. The linjk doesn't discuss the evolution of the flagellete at all. It just calls into question Behe's reasoniung about irreducicle complexity. See this is what, I mean. I wnat to know where the flagellete came from. There not telling me.

Anonymous said...

And the problemi have with thew Mullerian two step is that you hVE cells producing usedflles proteins, untilby a seredippipti accident, thney becoem usefull. Two accidents happeing for each protein. The flagellete has so,me thirty proteins. Each one absolutly necessary. So you need to have the Mullerian process repaeated thirty time. Also there are no known uses for half a flagellete. So you have to do the Mullerian thing thirty times at once.

Crawling Axe said...

And the problemi have with thew Mullerian two step is that you hVE cells producing usedflles proteins, untilby a seredippipti accident, thney becoem usefull. Two accidents happeing for each protein. The flagellete has so,me thirty proteins. Each one absolutly necessary. So you need to have the Mullerian process repaeated thirty time. Also there are no known uses for half a flagellete. So you have to do the Mullerian thing thirty times at once.

All of this is not true. I guess asking you to read again about the flagellum is pointless. Half flagellum does work — as a toxin injector, for example (or a similar function). You don’t need mutations to happen simultaneously. Read this.

Actually, a little while ago, I did correspond directly with Dr Theobald and he also was unable to answer my questions.

Perhaps he stopped responding when you started calling him names.

Crawling Axe said...

Imagine a conversation between R’ Yishmoell and R’ Akiva:

RY: They said “yes” and “no”.
RA: They said “yes” and “yes”.
RY: You say this because you’re a ba’al teshuva.

Why is this scenario impossible? 1) Because R’ Yishmoel would not use ad hominem attacks. 2) Even if he was right, so what?

jewish philosopher said...

There are no answers to my questions. Therefore, I question a little bit the motives of people who are not bothered by that.

Anonymous said...

"All of this is not true. I guess asking you to read again about the flagellum is pointless. Half flagellum does work — as a toxin injector, for example (or a similar function). You don’t need mutations to happen simultaneously. Read this."




Yes but it doesn't work as flagellete. I couldn't open the link so, I did some research on the topic on my own, again. I mentioned the Toxin shooter above. The shooter proteins have to mutate and change into flagellete proteins. And you need more proteins to make the flagellete, the rod , the cap, the filament, etc, and the special genes that control the contruction of the flagellete. So if they don't appear simultaniously, the cell has to wait with a non-functioning toxin shooter until they all appear. Of course some people have suggested that there may be some use for
the intermediate conditions, but this is conjectural.

And according to this link, there is some evidence that the toxin shooter evolved from the flagellette
http://www.newscientist.com/article/mg19726431.900-uncovering-the-evolution-of-the-bacterial-flagellum.html?page=3

Anonymous said...

This link?:
http://www.talkdesign.org/faqs/flagellum.html#update

Does have a scenario where a flagellete could have evolvd from a primnitve toxin shooter, but tis supposes a hypothetical primitive toxin shooter, and a whole bunch of fortuitous mutations happening at exactly the right time. And it supposes some purpose for the intemediates. And it doesn't discuss the special protein invovled in the construction of the flagellete, or the genes that time the construction. The flagellete is just one example. There are a lot more biochemical functions that are just as complex. There's DNA replication, protein synthesis, misosis, mitosis, etc. For each one they have to come up with a new "just so" story.

Anonymous said...

One last point. All these scenarios involve changing proteins. But the amino acids in proteins have to be arranged in a very precise sequence. It isn't so easy to change them and get something that works. You have to chaneg the active sites. You have to change the bonding sites. Its more than a simple mutation. If ts a something lke the flagellete propellor, then you have to chnage the whole thing.

Yeshivish Atheist said...

3/4 a flagellum is good for dispersion.

1/2 a flagellum is good for attachment to substrates

1/4 a flagellum is good for regulated protein secretion.

Why are we finding different beneficial functions when the flagellum is broken down? Doesn't sound so "Irriducibly complex" to me.

Secondly, the state of irreducible complexity can only tell us about the current state of the biological structure, not it's history because Reversing a mutation doesn't always mean you take a part out. Sometimes it means you put a part in. Sometimes it means you change an existing part.

The fallacy is just another straw man of evolution. It assumes evolution only gradually adds parts, which is not true. Evolution changes parts and can remove parts. Showing me something in which you can take 1 part out results in uselessness proves NOTHING unless you can somehow prove that the previous mutation added a part. But the previous mutation could have taken away a part, in which the correct thing to reverse the evolution in said biological structure would be to add the part back, not take a part out.

Unfortunately, with the part gone, how can one know what part to put back in? The whole thing is useless. You aren't proving anything by showing irreducible complex organisms, except that you know how to make a good straw man. you assume that evolution only adds parts, so the reversal of a mutation is to remove 1 protein. You forget that the reversal mutation could just as easily be to add a protein, which could no longer make said structure irreducibly complex.

Yeshivish Atheist said...

"The shooter proteins have to mutate and change into flagellete proteins."

The proteins that make the bacteria flagellum are so closely related genetically, to those that make up the secretory complex and bacterial pilli-- the genetic sequences are virtually identical. So they are just components of different systems that have been adapted for an alternate function.

"For each one they have to come up with a new "just so" story."

Oh give me a break. Who are you? William Dembski?

jewish philosopher said...

Honestly YA, I see no difference between an atheist claiming that all life developed spontaneously from a huge pool of water and minerals and someone like Cindy Anthony claiming that her daughter is with a babysitter. These are simply the flimsy lies of a psychopath.

Yeshivish Atheist said...

Wait a minute, I thought I was William Joyce. Now I'm Cindy Anthony??? Make up your mind.

jewish philosopher said...

You are a delusional psychopath who has rejected his religion for the sake of some trivial physical gratification.

Anonymous said...

Now they are sating that there is considerable evidence that the secretion system came from the bacterial flagellete. This means that they have to come up with anothetr scenario for the evolution of the flagellum.

Anonymous said...

"Unfortunately, with the part gone, how can one know what part to put back in? The whole thing is useless. You aren't proving anything by showing irreducible complex organisms, except that you know how to make a good straw man. you assume that evolution only adds parts, so the reversal of a mutation is to remove 1 protein. You forget that the reversal mutation could just as easily be to add a protein, which could no longer make said structure irreducibly complex."

Are yoy saying that a acomnplex structure can come from a ore complex structure? Then how does that more complex structure come from?

Anonymous said...

"The shooter proteins have to mutate and change into flagellete proteins."

The proteins that make the bacteria flagellum are so closely related genetically, to those that make up the secretory complex and bacterial pilli-- the genetic sequences are virtually identical. So they are just components of different systems that have been adapted for an alternate function.

But some amino acids ahve to change in very specific ways. And there are proteins that are unique the the falgellum. Where did they come from?


"For each one they have to come up with a new "just so" story."

Oh give me a break. Who are you? William Dembski?

Well, they hypothesis that a theoretical adehsion protein formed an attachment to the toxin tube. then it formed a ring. Then it formed some sort of propulsion system as the toxin was ejected. Then the motor proteins got borrowd from another purpose. Then the cap protein showd up. This means had to happen after the motor protein, because then it couldn't work as a propulsionm device or as a toxin shooter. See,alll thee accidents happening with perfect timing.

Anonymous said...

According to this study, the flagellum could not have evolved form the toxin shooter.



http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389

Moreover, there are regulatory genes that are specific to the flagellum that are critical to the assembly of the flagellum. These ahd to appear at th4 same time as the genes that code for the flagellum protein, or it won't work.

Yeshivish Atheist said...

"Are yoy saying that a acomnplex structure can come from a ore complex structure? Then how does that more complex structure come from?"

Irreducible complexity and complexity are not the same thing. In fact, some IC systems are quite simple and only involve some proteins, such as some cascade systems.

Sometimes, reversing a mutation can lead to more complexity and adding a part can lead to more complexity, but no longer irreducible complexity, thus further reductions will not result in no function.

In fact, IC bacteria have evolved over the past 70 years.

Pentachlorophenol (PCP) is a highly toxic chemical, not known to occur naturally, that has been used as a wood preservative since the 1930's. It is now recognized as a dangerous pollutant that we need to dispose of. But how?

A few soil bacteria have already worked out a way to break it down and even eat it. And conveniently for us, they do it in an irreducibly complex way. The best known of these bacteria is called Sphingomonas chlorophenolica (also called Sphingobium chlorophenolicum).

The PCP molecule is a six carbon ring with five chlorine atoms and one hydroxyl (OH) group attached. The chlorines and the ring structure are both problems for bacteria. S. chlorophenolica uses three enzymes in succession to break it down, as follows: the first one replaces one chlorine with OH. The resulting compound is toxic, but not quite as bad as PCP itself. The second enzyme is able to act on this compound to replace two chlorines, one after the other, with hydrogen atoms. The resulting compound, while still bad, is much easier to deal with, and the third enzyme is able to break the ring open. At this point, what is left of PCP is well on its way to being food for the bacterium.

All three enzymes are required, so we have IC. How could this IC system have evolved? First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally in small amounts. In fact the first and third enzymes were used for this. As a result the cell is triggered to produce them in the presence of chlorophenols. The second enzyme (called PcpC) is the most interesting one; the cell produces it in sufficient quantity to be effective all the time instead of just when it is needed in its normal metabolic role. Thanks to this unusual situation PcpC is available when it is needed to help eat PCP.

The inefficient regulation of PcpC is evidently the key to the whole process. So far as biologists can tell, a recent mutation that changed the deployment of this enzyme is what made PCP degradation possible for this bacterium. It also happens that both PcpC and the first enzyme in the process are now slightly optimized for dealing with PCP; they handle it better than the corresponding enzymes in strains of S. chlorophenolica that use PcpC only in its normal role, but not nearly as well as would be expected for an old, well adapted system. These factors, combined with the fact that PCP is not known to occur naturally, make a strong circumstantial case that this system has evolved very recently.


"But some amino acids ahve to change in very specific ways."

Irrelevant. If the genes are virtually indistinguishable than very little genetic change needs to occur.

"And there are proteins that are unique the the falgellum. Where did they come from?"

Yeah, out of all the required proteins, we only found 2 unique. whoopdey freakin doo.

"See,alll thee accidents happening with perfect timing."

All the accidents have been shown to have a beneficial function and involve one protein. It doesn't need to happen at perfect timing. If they went through all the accidents in other bacteria all the way that failed, it would be the longest paper on earth. Of course their only going to mention the important steps.

see http://www.youtube.com/watch?v=SdwTwNPyR9w

As for the pseudoscience institute, let them put their nonsense through peer review for a scientific jurnal. Oh wait, they don't. How convenient.

Anonymous said...

Changing the critical amino acids in a protein is certainly not irrelevant, even if the changes are minor. One misplaced amino acid causes sickle cell anemia. If they were still toxin shooter proteins, they would form a toxin shooter.

And in the article I mentioned on the cahnges needed to go from a toxin shooter to a flagellum, a whole bunch of proteins had to change drastically to go from a toxin shooter to a flagellum. The rod proteins have special mechanicakl qualities. Same thing with the linkage assembly, and the flagellin. Nothing like those in the toxin shooter. And same with the thing that assembles the flagellum at the tip.

And the timing of the accidents is crucial. If it developed the rod cap protein before it developed some propulsion function, then it wouldn't work as a propulsion device of a toxin shooter. And the same thing with the flageelin assembly mechanism. they had to show up at exactly the right time. And not just the genes that code for the protein. You need the genes that control the coding genes.

And the case of the bacteria you mentioned seems to be the result of just one mutation that in the gene that controls the production of the new gene. Thats easy.

Anonymous said...

According to this, they do publish in peer reviewed journals.


http://www.discovery.org/a/2640

Yeshivish Atheist said...

"Changing the critical amino acids in a protein is certainly not irrelevant, even if the changes are minor. One misplaced amino acid causes sickle cell anemia. If they were still toxin shooter proteins, they would form a toxin shooter."

If the genes are virtually indistinguishable, than it follows that only extremely minor genetic change can change the critical amino acid, so yeah, it is irrelevant, because it's not a problem.


"And in the article I mentioned on the cahnges needed to go from a toxin shooter to a flagellum, a whole bunch of proteins had to change drastically to go from a toxin shooter to a flagellum. The rod proteins have special mechanicakl qualities. Same thing with the linkage assembly, and the flagellin. Nothing like those in the toxin shooter. And same with the thing that assembles the flagellum at the tip."

Yeah, and in the link I showed you, all those changes down to each protein can be shown to be beneficial.

"And the timing of the accidents is crucial. If it developed the rod cap protein before it developed some propulsion function, then it wouldn't work as a propulsion device of a toxin shooter. And the same thing with the flageelin assembly mechanism. they had to show up at exactly the right time. And not just the genes that code for the protein. You need the genes that control the coding genes."

Do we find these examples in bacteria? If yes than the accidents are not specific critical timing since they happened in a non critical way in all the other trillions of bacteria, the accidents happened in a different order, so it's no surprise that it happened this way in at lease some of them. You are calculating sequential trials, not simultaneous trials, that is your problem.

If no, that on what basis can you say that if they happened in a different order they would be functional at all?? If that's the case than it's no surprise they evolved in this order.

Think simultaneous trials, NOT sequential trials.

"And the case of the bacteria you mentioned seems to be the result of just one mutation that in the gene that controls the production of the new gene. Thats easy."

The point is that we have proof now that evolution has produced irreducibly complex biological systems. So simply waving more IC systems in my face really doesn't phase me nearly as much now.

Anonymous said...

If the hook cap appears before the engine shows up, then it can't work as a propulsion device, or as a toxin shooter. Without the engine, the toxin going through the tube provides some torque, which provides some propulsion. But the cap blocks the tube so it can't be a toxin shooter, or a propulsion device. So it would have to show up after the engine appeared. The hook cap is crucial to the assembly of the hook. So the hook proteins have to show up at the same as the hook cap protein. Same thing with the flagellin cap. Both the flagellin and the cap have to show up at the same time. The flagellin serves no purpose wothout the falgellin cap to assemble the fillament. And each appearance of a new protein has to be accompanied by at least two genes, one to code for the protein, and one to code control the coding. The assembly of thew flagellum is very precisle controlled and timed.


And if youu have two preexisting parts then adding a third is easy. So that example isn't exactly comperable the the flagellum.

Yeshivish Atheist said...

The leading hypothesis for the evolution of the flagellum has it performing many different functions throughout its many transitional stages. Only in the very last stage does it acquire motorized power.

There are other beneficial functions along the way that you did not mention, such as dispersion, attachment to substrates, regulated protein secretion, controlled adhesion to substrates that allow bacteria to stay put where they want to, and more.

A Dr in Molecular Neuroscience actually took the time to make a video which answers most of your questions and explains this a lot better then I could.

http://www.youtube.com/watch?v=SdwTwNPyR9w&feature=channel_page

Yeshivish Atheist said...

"If the hook cap appears before the engine shows up, then it can't work as a propulsion device, or as a toxin shooter."

The toxin shooters, i.e. the non-flagellar Type 3 Secretion Systems, do not have hooks at all, and might not have caps (if some of them do, it does not have a strongly conserved sequence).

The flagellum (and the non-flagellar T3SS) grows as a tube by adding subunits to the tip. The cap sits on the growing tip and helps the new subunits insert.

There are (probably) 3 different caps used for growing different parts of the tube at different parts of the process. But the caps are not always required, e.g., FliD, the cap that is used for assembling all of the flagellin subunits (the major part of the flagellum tube, i.e. 99% of the mass of the whole flagellar system) is missing in e.g. Caulobacter.

So caps probably started out (and sometimes remain) just helpful for speed/efficiency, and only later became required in some systems some of the time.

See this table for which few flagellum parts are actually required and "unique" to the flagellum:
http://pandasthumb.org/archives/2006/09/flagellum-evolu.html

...although it is a little out of date, and a few more proteins are now known to be dispensible (FliI and FliH).

"Without the engine, the toxin going through the tube provides some torque, which provides some propulsion."

I've never heard this is possible, but if so, it's better for evolution...

"But the cap blocks the tube so it can't be a toxin shooter"

The cap, even if present, is/can be leaky. During flagellum assembly a bunch of copies of each of number of different proteins have to be secreted in this order: rod/cap/hook/cap/linker/cap/flagellin. The transitions between these are not perfect and units that no longer "fit" are just secreted out into the extracellular medium. Plus the cap "falls off" sometimes (or the flagellum is broken off & has to re-grow) & has to be re-secreted (probably, the cap protein is just continually secreted at a low frequency along with the common flagellin protein).

In any event, the cap proteins are known/suspected to be related to the flagellin/hook/rod proteins so their origin is not very mysterious.

"or a propulsion device. So it would have to show up after the engine appeared. The hook cap is crucial to the assembly of the hook. So the hook proteins have to show up at the same as the hook cap protein."

Not necessarily, see above.

"Same thing with the flagellin cap."

Definitely not true, the flagellin cap is missing in e.g. Caulobacter and yet the flagellum assembles anyway.

"Both the flagellin and the cap have to show up at the same time. The flagellin serves no purpose without the falgellin cap to assemble the filament."

No, the cap can be just a chaperone which helps, it is not necessarily crucial.

"And each appearance of a new protein has to be accompanied by at least two genes, one to code for the protein, and one to code control the coding."

Also not true, the control region (usually not a gene) can be copied along with the old gene. Or the new gene can just be stuck to "on" at some low level, which later evolves. There is a huge literature demonstrating the origin of new genes. Search google Scholar on "origin of new genes" for e.g. review papers by Manyuan Long. Any creationist argument that doesn't address & rebut these dozens of papers is simply incompetent, another example of creationists not doing their homework.

"the assembly of thew flagellum is very precise controlled and timed."

Sometimes, not always. There is a lot of variability in functional systems.

Anonymous said...

"The leading hypothesis for the evolution of the flagellum has it performing many different functions throughout its many transitional stages. Only in the very last stage does it acquire motorized power.

There are other beneficial functions along the way that you did not mention, such as dispersion, attachment to substrates, regulated protein secretion, controlled adhesion to substrates that allow bacteria to stay put where they want to, and more.

A Dr in Molecular Neuroscience actually took the time to make a video which answers most of your questions and explains this a lot better then I could."

he article I sicted said that the proto-flagellum had to have some torque in order to work as a propulsion device. It acquired the torque by the excretion of the toxin. It won't work otherwise.
And in order to function as something else, it has to be change in a very specific way.

The various caps are highly specialized to assemble their respective rods hooks and caps. What other function could they serve without going thri8gh a lot of very specific changes. And if the cap is there, it can't function as a toxin shooter.

And the control genes can't just be copied with their coding genes. They have to change in very specific ways in order to control the coding. And being stuck in "on"
won't work because the proteins are sent to the job site at exactly the right time,whne they are needed or it won't work.

Anonymous said...

And even if you can explain the bacterial flagellum, archaeobactria also have a flaggelum which is just as complex as the bacterial but is very different inb construction and form. And we've got the cilia in our lungs, and just about every structure and function. How do you explain all those? Do we just keep on getting lucky?

Anonymous said...

"The cap, even if present, is/can be leaky. During flagellum assembly a bunch of copies of each of number of different proteins have to be secreted in this order: rod/cap/hook/cap/linker/cap/flagellin. The transitions between these are not perfect and units that no longer "fit" are just secreted out into the extracellular medium. Plus the cap "falls off" sometimes (or the flagellum is broken off & has to re-grow) & has to be re-secreted (probably, the cap protein is just continually secreted at a low frequency along with the common flagellin protein)."

But if the cap is leaky it will still prevent the toxin from being succreted efficiently and effectively. And if it falls off too soon, it can't function as a cap. It has to be biologically useful.

Anonymous said...

An dit sno simple tasl to change form one protein to another, evenhomologous proteins. You ahve to change just the right amino acids.

Anonymous said...

Now to change from one protein to another, you have to change at least nine amino acids out of hundreds (unless I'me very much mistaken). Three for each of the binding sites, and three for the active site. That's no easy feat.

And saying that the flagellum had interum function on its way to becoming a flagellum without expaining the mechanics of how it functioned is not quite enough. Every structure, eg the bacterial pili is engineered for a specific function, and without that engineering it won't work. You have to explain how it could work. The report I sited above does that. But just to say it had lots of functions without explaining how, doesn't cut it with me.

Anonymous said...

But if the cap is leaky it will still prevent the toxin from being succreted efficiently and effectively. And if it falls off too soon, it can't function as a cap. It has to be biologically useful."

According to the article sited above, it is the secretion of the toxin that gives the toxin shooter a torqures that allows it act as a propulsion device. It has to secrete efficiently for this to happen. If it just leaks out because the cap is there at the wrong time, you don't get enough torque.

Anonymous said...

I did a little research on analogous proteins. It seems that they can have quite different amino acid sequences, and still be considered homologous. Sometimes it is the similarity in the tertiary structure that gives the calssification. Now that being the casse, for flagellum proteins to evolve from homologous proteins would still require a large number or very specific changes in the sequnce of amino acids. Againn ,we keep on getting very lucky.

Anonymous said...

So the genes from that coded for the proteins that evolved into flagellum proteins were copied withtheir control sequences in a low level "on" configuration, which? See, we keep getting very lucky.