lucaspa

lucaspa, you are misinformed on what it takes to be biologically alive. To be biologically alive, your prebioants (which is exactly what they are) must be subject to natural selection.

That's not part of the definition of "life". But, as it happens, the protocells I'm talking about (did you read the websites?) are subject to natural selection:

"The ease with which such protocell units arise under possible primitive Earth conditions has been abundantly documented, especially in the elegant experiments of Sidney Fox and his collaborators on the proteinoid microspheres. .. For our purposes it is sufficient to note that preformed primitive polypeptides (proteinoids) have properties enabling them to aggregate spontaneously to form remarkably uniform spherical units of bacterial dimensions which contain complex internal morphology including a double wall, exchange materials with the ambient medium, grow, cleave in two, fuse, exhibit weak catalytic activiity, and move when ATP is added to the medium. Protocells containing both proteinoid and polynucleotide have been shown to carry on a primitive kind of protocoding activity (27,29) The proteinoid microsphere is a compelling model for the high-probability prebiotic origin of discrete individual units of evolving organic mattter which could conceivably compete with one another and thus provide the basis for a primitive selection process." Dean H. Kenyon, Prefigured ordering and protoselection in the origin of life. In The Origins of Life and Evolutionary Biochemistry, ed. Dose, Fox, Deborin, and Pavlovskaya, 1974, pg 211.

Whatever they were, those protocells, they were non-living chemicals—biologically non-living, that is—and probably extremely rare.

Wrong on both counts. The protocells would be living. To be alive, an entity must have all 4 of the following characteristics:

1. metabolize (have anabolism and catabolism)

2. Grow

3. Respond to stimuli

4. Reproduce.

Crystals grow, but they don't do the other 3. Protocells do all 4. They are that "magical moment" when life began and Darwinian evolution started.

I am talking about what was necessary for that splendid moment to occur—the one when a genetic language kicked in and those prebiotic protocells took on the job of genetic inheritance. That's when biological life began; that's when abiogenesis occurred.

Strawman. Genetic inheritance is not needed to be alive. Abiogenesis happens before the beginnings of genetic inheritance.

Please consider this from A. G. Cairns-Smith’s Seven Clues to the Origin of Life (1985, pp. 114-116):

 

“First clue: Genetic information is the only thing that can evolve through natural selection because it is the only thing that passes between generations over time...”

With all respect to Cairns-Smith, that isn't true. The protocells will vary between individuals, because they will have different proteins within them. Some of those individuals will have proteins with higher catalytic activity than others -- including activity to make more proteins. Daughter cells will also differ, because as the cell fissions, each daughter will end up with a slightly different composition. So now we have natural selection working favoring those protocells that 1) metabolize better and 2) reproduce faster.

As such, all biologically living things owe a debt of gratitude to your prebioants, but however splendid they are they don't represent what happened when abiogenesis became a reality.

You keep repeating this, but you don't give us any data on how the protocells are not alive. Except for your strawman insistence on having directed protein synthesis. Again, several papers have shown how that can arise later.

Since you like to quote but not read data, here' Fox's sequence of early life:

1. Formation of amino acids from primordial precursors (water, ammonia, carbon dioxide, methane, oxygen, hydrogen, etc.) [M-U experiments and Miller and Orgel].

2. Formation of proteinoids by polymerization of sets of amino acids. [Fox and others].

3. Formation of protocells by contact of proteinoids with water [Fox and others]. (this is abiogenesis)

4. Synthesis of RNA within the microspheres [Fox]

5. Replication of RNA. [Orgel]

6. Development of the genetic code.

Consider this paper:

1. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J. Molecular Evolution 46: 1-17, 1998.

It describes a Darwinian step-by-step evolution from RNA molecules to directed protein synthesis. All intermediate steps are useful. Once you have protocells that are making RNA (as it has been shown protocells do), then directed protein synthesis (what you call the "genetic code") is going to follow -- as a product of evolution. Not the start of evolution, but the product of Darwinian evolution.

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Wait, isn't that cheating just a bit? We need to induce cleavage?

That was a quote from a 1975 biology book. It turns out that, when the protocells grow to a critical size, they divide on their own.

I thought you said that some of them are photosynthetic. Are all of them photosynthetic?

Bahn PR, Fox SW. Models for protocellular photophosphorylation. Biosystems. 1981;14(1):3-14.

Masinovsky Z, Lozovaya GI, Sivash AA, Drasner M. Porphyrin-proteinoid complexes as models of prebiotic photosensitizers. Biosystems 1989;22(4):305-10.

Masinovsky Z, Lozovaya GI, Sivash AA. Some aspects of the early evolution of photosynthesis. Adv Space Res 1992;12(4):199-205.

It turns out that porphyrins (and chlorophyll is a porphyrin) are also made when amino acids are dry heated. Initial studies didn't look at porphyrins. Remember, when you make protocells, you are going to make at least a million of them. Some of those will have porphyrins such that they are photosynthetic.

No, the protocol is quite simple, but as I said I don't want to make my own. I want to grow a colony of them from a sample of protocells, especially ones with interesting properties. You know, like culturing strains of bacteria?

Well, you are going to have to make your own. The protocol is so simple that this is what people have been doing: making up batches of protocells as needed for testing. So make up your own batch and then make strains if you wish.

Well yes, this is done in undergraduate level biology classes. Probably some high schools too. Eg for teaching aseptic technique, they have you inoculate a plate with distilled water. If something grows, you did it wrong (or were unlucky).

You need something more than distilled water. You need an energy source -- such as glucose. All the protocols I've seen use bacterial agar or sterilized salt solutions with sugar.

I test the students' sterile technique by changing culture medium every day for a week using a biological safety cabinet. But I am old enough to have been around in the days of dead air hoods. Those routinely had a fairly high rate of contamination and people did not keep continuous cultures for more than a few weeks. If you want to generate strains of protocells, you are going to need more than a month. Good luck.

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Are you referring to flavoprotenoid microspheres or about lipid protocells?

I'm referring to protocells made from 1) thermal polymerization of amino acids to proteins and 2) the addition of salt solution. For the umpteenth time, here are 2 websites for you to start on. Just read them.

http://www.theharbinger.org/articles/rel_sci/fox.html

http://www.siu.edu/~protocell/

We can go into more detailed papers after you read the websites.

In flavoprotenoid microsphores ATP generation was found but essentially it was due to irradiation of ADP in presence of Pi (which is quite intersting by itself, though), but I have not yet heard about real photosynthesis.

Could you provide a source for that ?

See the 3 papers I quoted earlier in this combined post.

And why precisely would one need a culture medium for them? I may be missing something but they do not have metabolism and hence should be pretty stable in a defined buffer. Am I missing something here?

The protocells I'm talking about do have metabolism, so you need a source of sugars, amino acids, and nucleotides. IOW, what you would find in the pre-biotic environment.

I'll explain, the data we have that suggests the universe is expanding at an everincreasing rate comes from modern observations of photons which started their journey towards us up to 12 billion years ago,

No, the data comes from supernovae in galaxies much closer to us than 12 billion light years away (see references below). Plus, add the fact that there isn't enough matter in the universe to cause the contraction plus add the fact that there is a repulsive force causing the expansion to accelerate.

All this adds to the inference that the universe is going to expand forever and never contract. There simply is no force to make it contract.

BTW, rubber bands cannot expand infinitely. Any sapient species is going to find the modulus of elasticity of a rubber band. Yes, materials have things like Young's modulus, stress vs strain curves, etc. All of these show limitations to the elasticity of materials.

Some references with the data for you to look up to verify the summaries of conclusions I have given you:

5. A Watson, Clusters point to a never-ending universe. Science, 278: 1402, 21 Nov. 1997. Discusses paper that will appear in Astronomy and Astrophysics about the clusters that bend light from distant objects. The model predicts the number of such clusters we should see. With 33% of the critical mass the model predicts 2500 clusters. We see 2300-2700. Up the mass to the critical value and the predicted number drops to 25.

6. JP Henry, UG Briel, and H Bohringer, The evolution of galaxy clusters. Scientific American 279: 52-57, Dec. 1998.

7. Lineweaver CH and Davis TM Misconceptions about the Big Bang, Scientific American 36-45 March 2005. http://www.sciam.com/article.cfm?chanID=sa006&colID=1&articleID=0009F0CA-C523-1213-852383414B7F0147

7. J Glanz, Exploding stars point to a universal repulsive force. Science 279:651-652, 30 Jan. 1998. New data indicates the cosmological constant is back.

7a. J Glanz, No backing off from the accelerating universe. Science 282: 1249-1250, Nov. 13, 1998. As the title says, 2 independent and competing groups continue to get data that agrees.

8. G Tarke and S.P. Swordy, Cosmic Antimatter. Scientific American, 278(4): 36-41, April 1998.

10. CJ Hogan, RP Kirshner, and NB Suntzeff, Surveying space-time with supernovae. Scientific American, 280: 46-51, Jan. 1999. Studies indicate that the rate of expansion of the universe is accelerating.

11. LM Krauss, Cosmological antigravity. Scientific American, 280: 52-61, Jan. 1999. discusses cosmological constant to explain accelerating expansion.

13a. Web sites for expanding universe

http://www.cnn.com/TECH/space/9802/...ating.universe/

http://www.space.com/scienceastrono...celerating.html

http://www.er.doe.gov/Sub/Accomplis...scovery/43.html

4. J Glanz, Microwave hump reveals flat universe. Science 283: 21, Jan 1, 1999. Data on microwave background radiation indicates that universe is flat.

24. http://www.lpi.usra.edu/publications/newsletters/lpib/lpib77/black77.html Website has equations to calculate age of universe

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I did read that the expansion will continue until the average temperature of matter comes within one planck degree of absolute zero, at which time the matter will dissappear,

And where did you read that matter will disappear? Why should it? From what I have read (see references above), the data right now indicates that the universe will expand forever and eventually go into "heat death". That is, all the fusable material in stars will be used up, they will cease to shine, and the temperature of the universe will go toward absolute zero. Also, as space continues to expand, evetually no part of the universe beyond the solar system will be visible to us. Scientific American had an article on this a couple years ago entitled "The End of Physics".

Not to delve too far into science fiction, but while I'd agree for Terminators, I'm not so sure for Cylons. Given a LOT of time, and a lot of technological advances, it may be possible to create a robot that operates at such a fine scale that its operating units are much like cells, and it has similar capabilities.

There was always a question whether the 12 were machines or biological organisms. Since BSG had a Cylon and an H. sapiens having a fully fertile offspring, that would make those Cylons and H. sapiens the same species! It also meant that they were no longer robots but were using biological chemicals, i.e. DNA instead of circuits.

Alternatively, could non-growing, non-reproducing robots produced by an automated factory be considered 'life' in much the same way as a bee hive, functioning as a sort of 'superorganism'?

Good question. But notice "factory" Bees are still reproducing by processes within (at least a specialized) bee. Not a separate factory.

However, I do agree that it's moot, since such machines would need a non-mechanical race to create them in the first place.

Yeah. Still no natural process to manufacture the first one.

What I think would happen is that the definition of "alive" would end up changing (despite Mr. Skeptic's attempt in Politics to have a definition frozen) to include anything that was sapient. Star Trek explored that idea both with Mr. Data in TNG and the Doctor in Voyager.

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A simple matter of scale. The robots would have to reproduce or they would die out.

Not necessarily. Remember, individual parts can be replaced so that a robot would, for practical purposes, be immortal.

 

But our current definition of "alive" means the individual has within itself the means to grow and reproduce. A factory is not within the individual.

 

But some chemical life could make the robots and then the robots wipe out their creators.

 

That doesn't change the fact that robots ultimately are a manufactured entity -- no process in the environment could produce a robot. Chemistry can produce a biological organism.

 

I could, however, see limiting "life" to chemical processes only.

 

From your posting in Politics, to be internally consistent about definitions you personally would have to.

 

I mostly mentioned them as they could satisfy the criteria for life, but clearly don't need water.

 

That's the problem. They don't satisfy the criteria for life. We would have to change the definition before they could qualify.

I tend to agree with waitforufo. Definitions change. Look at the definition of "citizen" over the centuries. Or the change in qualifications that defined "voter". Definitions are a consensus of what a word means at the time. That consensus can change.

However, these sites give a history marriage:

http://marriage.about.com/cs/generalhistory/a/marriagehistory.htm

http://molly.kalafut.org/marriage/marriage-types.html

This article is by an historian specializing in the history of marriage:

http://hnn.us/articles/4400.html

This article summarizes laws regarding same-sex unions in all the countries of the world:

http://molly.kalafut.org/marriage/world-laws.html

Why? That's my point. Why would the designer do it? I doubt that we would understand the answer.

So that life would evolve such that it would be able to communicate with the designer! That's one hypothesis for "why" that is easily arrived at.

I think what you are trying to do is use an unanswered question on the next level to deny a possible answer on the level above it. Let me explain: every time you answer a question, 3 or 4 new questions pop up out of the answer. You don't have answers to those new questions, but you can't use that fact to deny the answer you already have. For instance, 25 years ago Marshall Urist found that demineralized bone matrix would cause the formation of bone outside of existing bones. He then showed that the responsible agent was a protein. Which protein? What cells did it react with? How did the protein react with the cells? All these questions popped up out of the answer and we didn't know the answer to any of them. BUT, we couldn't deny that a protein caused extraskeletal bone formation.

In this situation, we have the question: what's the origin of the universe? Possible answer: an ID (deity) created it by means that we don't understand. New questions: what is that ID like? Why would the ID have created a universe? What's the origin of the ID? None of those have any relevance to the possible answer. IF we ever show that the universe was created by an ID (deity), then we will have to tackle those questions. But it appears that you are using the presence of those future questions to deny the possible answer. You can't do that.

Not neccessarily, if looking for data either way, it would be helpful to know what you are looking at.

It's irrelevant that the ID would be very advanced if the question is whether the universe was created (manufactured) by an ID (see above).

If there was a designer, it is reasonable to assume that the proof is in the fine structure of the bottom, not the ripples on the surface.

Not necessarily. The way we conclude manufacture by an intelligent entity (which is really what ID is all about) is to look to see if there is any natural process that could produce the entity. If there is, then we can't conclude manufacture.

In terms of the two questions about the universe itself, we don't have that "natural" process. Therefore the possibility of direct manufacture via Big Bang can't be eliminated. After the universe gets here, then we do have "natural" processes to produce the entities within the universe. As Hawking put it:

"Even if there is only one possible unified theory, it is just a set of rules and equations. What is it that breathes fire into the equations and makes a universe for them to describe? The usual approach of science of constructing a mathematical model cannot answer the questions of why there should be a universe for the model to describe. Why does the universe go to all the bother of existing? Is the unified theory so compelling that it brings about its own existence? Or does it need a creator, and, if so, does he have anyother effect on the universe?"

Stephen Hawking, A Brief History of Time, pg 174.

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Could it be that we and our universe were intelligently designed by transhumans?

The universe, possibly. Ourselves? No. We are the product of natural selection as the designer. Life arose by chemistry, not by manufacture.

However, it's possible that some intelligent entity (H. sapiens in the far future) could devise a technology that would bring a universe into existence. In that sense the universe as a whole would be manufactured.

Very small statistical fluctuations could, in some limited locality, bring about a solar system with huge amounts of boron or some other chemicals that are even more conductive to life than carbon and or water.

I think those would be at the far end of the bell-shaped curve. We can get an idea of the relative abundance of elements in a solar system by analyzing the spectrum of the star. After all, both the star and its planets formed from the same nebular cloud. So, do you know of any stars that have an abundance of boron?

That life might get along great without the things we think life has to have and maybe these other chemicals react in ways we are unaware of that makes life much easier with that chemical.

That presumes we have a huge gap in our knowledge of chemistry! The evidence suggests we don't have a large gap. After all, chemists have been trying out possible combinations of chemicals for over 300 years, using more and more exotic conditions. So, the odds are that, if boron polymers are easily made, we would have made some before now.

I agree we only have one data point about life, but we have many data points about chemistry. And life is, essentially, chemistry.

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Well, I could consider a sufficiently advanced robot to be life. However, I think that robots would have to be intelligently designed, so they'd also need some chemical-based life to make them.

1. A sufficiently advance robot would be considered sapient, but not necessarily "alive". It probably would not have internal mechanisms either for growth or reproduction.

2. I don't see any natural process in the universe that could produce an AI. If nothing else, there is no natural process to refine the metals that go into the body of the robot and the semiconductors or chips. So yes, ultimately robots are artifacts manufactured by a chemically-based lifeform.

You need to take a better look at what you’re saying. I don’t even know what you mean by “non-living chemicals.” Is RNA a non-living chemical? Is NaCl a non-living chemical? I’d say both are non-living chemicals, including DNA.

Then we don't have a problem. IF you would have read the websites (did you? It appears not.) then you know we aren't even starting with RNA or DNA or proteins. The starting chemicals are amino acids, the precursors to proteins.

If you know of a living system that gets along in life without genetic information I’d love to hear about it.

I'm telling you about one! Read the websites! Protocells do not have a genetic system but they do have, in a fashion, a system of inheritance.

OK, I’ll assume from what you say that the “needed” proteins can be made directly with AAs and heat. But that doesn’t get you abiogenesis from scratch.

If you then add water to the proteins, that does get you abiogenesis from scratch. Read the websites! Directed protein synthesis comes later. The protocells make RNA and DNA from nucleotides.

Reproduce what? You’ve haven’t even addressed the need for the emergence of a digital genetic code.

Themselves. New protocells. There is no need of a genetic code to have life. That comes later. By division, the protocells do pass on their materials to their progeny.

You cannot have abiogenesis until you have a cell with the ability to pass on its genetic material to its progeny.

That's your strawman. Being alive only calls for reproduction. It doesn't call for "genetic material". That's your fixation: that you think you have to have DNA/RNA and directed protein synthesis from the beginning. You don't. They can come later after you have living cells. See the quotes at the end of the post.

I’m astonished that one in your position would say this. If what you say is true then please show the evidence that those little gene-less critters actually did pop out as the “bottom line.”

Read the websites! Part of the evidence is there. After you have read the websites, I'll direct you to some peer-reviewed articles in the scientific literature.

I’m still wondering how you can get “reproduction” in life without being concerned about genetic inheritance. Do your “protocells” just sort get their genetic information by osmosis?

LOL! The protocells divide. Like bacteria. Each daughter cell gets half the material of the original. Then they too grow in size until the point that they, too, fission. Read the website. It's all there if you would have taken the time to look at the data.

This statement is unbecoming of a “Biology Expert Moderator.” How can you refute my claim of being an untheist? Who would know better than I?

People can mislabel themselves. You can start by addressing the issues I raised. Why is it that you are objecting so much to any suggestion of life arising by simple chemistry? Resisting to the point that you won't even look at the sources given you.

Suggesting that I am a creationist is shameful, worthy of suspension.

If it walks like a duck and quacks like a duck .... Saying abiogenesis is impossible is one of the major arguments and claims of creationism. I think you'd better look in the mirror before you throw around the charge of "insecure". Why haven't you read the websites I posted? If you had, you wouldn't have posted this silly post, because all the answers were there.

"Self-forming, cell-like structures ... have been described, in great detail, by Fox. These remarkable bodies arise spontaneously wehn hot concentrated solutions of thermally formed proteinoids are allowed to cool .... Microspheres show several types of cell-like behavior. They can be induced to undergo cleavage or division by suitable changes in pH or when exposed to MgCl2. ... They can also be shown to accelerate chemical reactions when formed from proteinoids having catalytic activity ...

In more recent work, Fox and his colleagues have shown that basic proteinoids, rich in lysine residues, selectively associate with the homopolynucleotides poly C and poly U but not with poly A or poly G. On the other hand, arginine-rich proteinoids associate selectively with poly A and poly G. In this manner, the information in proteinoids can be used to select polynucleotides. Morever, it is striking that aminoacyl adenylates yield oligopeptides when incubated with proteinoid-polynucleotide complexes, which thus have some of the characteristics of ribosomes. Fox has suggested that proteinoids bearing this sort of primitive chemical information could have transferred it to a primitive nucleic acid; the specificity of interaction between certain proteinoids and polynucleotides suggests the beginning of the genetic code." A. Lehninger, Biochemistry, 1975, pp 1047-1048

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But I want to grow a colony from one of yours, not make my own. I have no idea what properties mine would have.

The literature on protocells (sometimes called "microspheres") is quite extensive. They all have the same properties; the properties are not dependent on colonies. So if you make your own they will be like all those in the literature.

I don't have a colony of them right now. I made a batch just to see that I could, if I followed the protocol in the literature. Do you think the protocol I have laid out is too complicated for you to follow?

And yes, I am familiar with aseptic technique. I don't have a flow hood but I have usually been able to avoid contamination by leaving things uncovered for a minimum time.

Really? I'm a bit skeptical since I have seen people, even using dead air hoods, have a pretty high rate of contamination. But hey! That's a problem of contamination and technique, not the cells. So go for it. I would use standard culture media, probably CMRL 1066 or BGJ. Or you could use bacterial agar. Have fun. BTW, if you use culture media, then changing media is going to be a bit difficult, since the protocells are the size of bacteria and don't adhere to the culture dish. It's like dealing with suspension cultures. But you sound like you think you know what you are doing.

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Furthermore, I don't think panspermia helps as much as you'd think.

I don't think it helps at all. It simply pushes the problem to someplace else (sometimes called "begging the question"). That life off earth had to come from somewhere. Where? Where did life arise if not on earth? How did life arise in this other place? Chemistry? Manufacture by aliens? If the latter, how did the aliens arise? If Scrappy doesn't think the genetic code could have arisen by chemistry and biology on earth, why would he think it could arise someplace else?

Somewhere you still face the issue of abiogenesis: life arising by chemistry.

Given that early Earth wasn't a homogenous mass, you could probably find some or many of the 'extraterrestrial' conditions here, such as under ice or near deep-sea vents.

Good point. The earth has some extreme environments, about as extreme as they can be and still have liquid water.

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Thank you for pointing out my hang ups. And you are quite right: I am terribly hung up about the need for a digital genetic code to arise (however mysteriously) in the course of any abiogenesis event.

That's your misconception. You don't have to have a genetic code at an abiogenesis event. Directed protein synthesis can come later and evolve.

Your little “prebionts” in their lipid bubbles, how do they accomplish reproduction without a genetic language? Just simply duplicating themselves in chemical composition is not enough; calcite crystals can do that.

No, division is sufficient. You don't have to have "coded instructions". All you have to have are the elements that allow the progeny to by alive. Elements for metabolism, response to stimuli, growth, and let the progeny themselves reproduce. "Coded instructions" can come later.

Could you send me one of these living protocells and a list of their nutritional requirements? I'd like to grow my own colony of them from one of yours.

You can make your own. It's very simple. Here's the recipe:

Call Sigma Chemical Co. at 800-325-3010 and order 1 bottle of catalog number M 7145 and one bottle of R 7131 amino acids solutions (you need both to get all the amino acids http://www.sigmaaldrich.com/sigma/formulation/M5550for.pdf ). They will cost you about $40 plus shipping for both. Empty the bottles into a fying pan, turn the heat on low and heat until all the water is evaporated. Then heat for 20 more minutes. Add water.

You can then add more amino acids, some ATP, and some sugars if you want. However, it turns out that some of the protocells are photosynthetic.

You are going to have a minor problem: bacterial contamination. Bacteria are everywhere and, if you leave the protocell solution sitting out for even a couple of minutes, bacteria from the air, your spoon, etc, is going to get into the solution and these bacteria will, in about a day, eat the protocells. So, do you have a laminar flow hood and some culture dishes?

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Yes, I’ve taken biology. I have a Ph.D. in biology. Anyway, you say base pairs are “attracted to each other”? I never learned about any such "attractions" in the chemistry courses I ever took.

Then you don't have a Ph.D. in biology! Any Ph.D. would immediately recognize the phrase "attractions" to mean the hydrogen bonding between complementary bases.

So, I might ask you if you have every read the crucial paper by F. H. C. Crick, “The Origin of the Genetic Code” (1968, J. Mol. Biol., pp. 367-379). If you had you would see why proponents of the stereochemical theory face “grave difficulties”:

 

 

If you could get a copy of this paper through your public library (I don't know of an Internet source) and read it carefully, you would see why the origin of the genetic code is not so easily dismissed as perfunctory.

The public library will not have a copy of the paper. But notice that the paper is 1968. Here are some more recent papers for you to read that show how the genetic code can easily have evolved:

1. Alberti, S The origin of the genetic code and protein synthesis. J. Mol. Evol. 45: 352-358, 1997.

1. AM Poole, DC Jeffares, D Penney, The path from the RNA world. J. Molecular Evolution 46: 1-17, 1998. Describes Darwinian step-by-step for evolution from RNA molecules to cells with directed protein synthesis. All intermediate steps are useful.

2. P S Schimmel and R Alexander, All you need is RNA. Science 281:658-659, Jul. 31, 1998. Describes research showing that RNA in ribosomes sufficient to make proteins. Intermediate step in going from abiogenesis to genetic code.

3. http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030139 Paper showing evolution of stable proteins.

4. Margaret E. Saks, Jeffrey R. Sampson, John Abelson Evolution of a transfer RNA gene through a point mutation in the anticodon. Science, 279, Number 5357 Issue of 13 March 1998, pp. 1665 - 1670

I like to postulate new ideas in the realm of science, but find there is a rule that speculations must be backed up by evidence or some sort of proof.

 

Does anyone beside me find this rule "just wrong"?

Yes. That rule is based on a refuted philosophy of science called Positivism. It held that entities had to be "verified" before they could be considered as existing. Entities included hypotheses/theories.

In actuality, in science nearly all hypotheses/theories are proposed without evidence! You propose them first and then go looking for the evidence to test them. The object of the testing is to show the idea to be wrong.

"I thought that scientific theories were not the digest of observations, but that they were inventions -- conjectures boldly put forward for trial, to be eliminated if they clashed with observations, with observations which were rarely accidental but as a rule undertaken with the definite intention of testing a theory by obtaining, if possible, a decisive refutation." Karl Popper, Conjectures and Refutations, 1963 p 38.

For example, am I correct that to speculate that space preceded the Big Bang would not be allowed because there is no evidence, no proof, and no currently feasible test?

That would seem to be the case. Although that means that Martin Bojowald is not doing science.

The Speculations Policy ends with the encouraging line, "Have fun". Am I being overly cynical to suspect that is said "tongue in cheek" ?

No. I think the problem here is that too many people come here with "speculations" that are not tentative and that they are not willing to give up. How firmly comitted are you to this idea that space existed before the BB? If you are not willing to listen to evidence falsifying it, then conversation with you isn't going to be "fun". So the proscription may have been to at least make you test your idea a bit before you post it.

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We know energy is a characteristic of mass and can be used by extracting it from mass, as in burning coal to boil water to turn a turbine to operate machinery. That process converts energy from coal to useful motion. Agree? … Good.

As several people noted, this is energy in chemical bonds, not differences in mass! If you want E = mc^2 to apply, you are into nuclear fission or fusion.

Does everyone agree that there is a precise equivalence instead of an imprecise casual variable type of relationship between energy contained within mass and the useful energy that is extracted from mass?

No. Now you are into entropy. When you say "useful energy" you are saying "energy available to do work". So now you are talking about entropy. There is not an "equivalence" but very precise equations relating the "useful energy" to the total energy.

And if energy quantization is the way that equivalence is achieved by nature, wouldn't it follow that the fundamental particles would contain energy in quantum increments, implying that the various fundamental particles all have something in common, and that commonality is energy quantization.

Fundamental particles do have something in common: they are composed of quarks.

At some level, energy in atoms is quantized, but not the energy of mass you are thinking about: http://www.chm.bris.ac.uk/pt/allan/allan1a.htm

Atoms and electrons within atoms can exist only at particular quantized energy states. However, I have never heard of E = mc^2 + p^2c^2 being quantized. The energy we get from nuclear explosions or nuclear reactions does not seem to be quantized. That research -- nuclear weapons and nuclear reactors -- would be the place I'd start if I wanted to find evidence that E = mc^2 was quantized.

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the M in E-M-E is matter and matter is said to form within every arena during its expansion phase from dense dark energy.

 

So if matter does form from dark energy

You need citations to the scientific literature here. I have never seen anything that says matter arises from dark energy. Dark energy is the term used to describe the repulsive force that is responsible for the accelerating expansion of the universe.

So, you need to document your "if". Everything after that depends on this being true, so you have to document that it is.

Remember that the big crunch formed as a result of the intersection and overlap of two or more expanding arenas.

All the evidence now says there was no "big crunch". The universe is just going to expand forever. Nor have I seen anything about "the intesection and overlap of two or more expanding arenas" Again, you need citations to the scientific literature. Without those this discussion stops dead in its tracks.

We have dark matter in the form of energy quanta separating and moving away from each other due to the expansion momentum imparted to them as they formed,

Again, the data I have seen contradicts this. Dark matter seems concentrated in galaxies and is not "moving away from each other". Again you must have a scientific citation to back this statement.

Yeah, this is discussing a theological position within Christianity. It's not the only theological theory about the crucifixion and resurrection, either. Inquisitor, you need to take this to a Christianity forum somewhere so you can have an appropriate theological discussion about it.

In the bible, the universe is created in six days. (in the seventh day God resteth...)

 

Now, many say this cannot be so. I say, why not? It is possible, but only if we see the world as a computer generated simulation....

The same could be the case with our universe. It could well be a simulation inside a complex AI machine brain the size of a planet.

The problems with this idea are theological, not scientific. Science can't address this. Yes, it's possible, just like we could be living in the Matrix -- which also is a computer simulation.

However, religion must reject it because it has God lying to us. All the evidence of our senses says there is a real, objective universe out there, not a computer simulation. What's more, that evidence says the universe is billions of years old and developed over those billions of years. If you accept this idea, you have made God a colossal liar. But theists rely on God being truthful about things that matter a great deal to theists: salvation, forgiveness of sins, an afterlife, etc. But if God can lie to us about the nature of the universe, you can't trust God about these things.

No, it's not going to be science that rejects this idea, but religion. In fact, religion already rejected it. Basically, this is a variation on the Oomphalos argument. That was decisively rejected in 1858 and the decade afterward. While it preserves a 6 day Creation, it destroys God.

I know bringing up the idea of the possibility of an intelligent designer of the universe on a science forum is not exactly a good idea.

 

My case (in a totally a non irreligious way) could be the exactitude of the cosmological constants, that if even one differed minutely we would never have come into existence

There are two questions in science where it is still possible to hypothesize direct action by an "intelligent designer". You have hit upon one of them:

Why is the order of the universe the way it is instead of some other order? Hypothesis: an ID (or deity) created it this way.

The other question is: Why does the universe exist at all?

Hypothesis: an ID (deity) created it.

The problem is that there are a number of alternative hypotheses to the second question. We don't have sufficient data to rule out all but one of them.

In order to get a "scientific case" for the ID hypothesis to the first question, you must invoke the Strong Anthropic Principle. The SAP basically says the universe must have the constants it does. But that is simply bad logic:

"According to the Anthropic Principle, we are entitled to infer facts about the universe and its laws from the undisputed fact that we (we anthropoi, human beings) are here to do the inferring and observing. The Anthropic Principle comes in several flavors.

In the "weak form" it is a sound, harmless, and on occasion useful application of elementary logic: if x is a necessary condition for the existence of y, and y exists, then x exists. If consciousness depends on complex physical structures, and complex physical structures depend on large molecules composed of elements heavier than hydrogen and helium, then, since we are conscious, the world must contain such elements.

"But notice that there is a loose cannon on the deck in the previous sentence: the wandering "must". I have followed the common practice in English of couching a claim of necessity in a technically incorrect way. As any student in logic class soon learns, what I really should have written is: *It must be the case that*: if consciousness depends ... then, since we are conscious, the world *contains* such elements.

The conclusion that can be validly drawn is only that the world *does* contain such elements, not that it *had* to contain such elements. It *has* to contain such elements *for us to exist*, we may grant, but it might not have contained such elements, and if that had been the case, we wouldn't be here to be dismayed. It's as simple as that.

Take a simpler example. Suppose John is a bachelor. Then he *must* be single, right? (That's a truth of logic.) Poor John -- he can never get married! The fallacy is obvious in this example, and it is worth keeping it in the back of your mind as a template to compare other arguments with."

Daniel Dennett, Darwin's Dangerous Ideas, pp. 165-166.

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In the case of the Universe, we have no idea what it was designed for, f it was designed.

The issue is usually stated that the universe seems designed for life. If any of a myriad of physical constants were just a bit different, life would be impossible. Since those constants seem arbitrary, why do they have the values they do? Thus the hypothesis of direct manufacture and choice by an ID (deity).

Of course, there is no mandate that the universe must have those constants (see logical argument above). If it did not, we simply wouldn't be here to wonder about it.

And, one of the reasons String Theory is so attractive is that most of those constants have their values determined by the properties of strings and 'branes, thus removing the problem.

A major problem with the idea of an Intelligent Designer is that any entity with the power, lifespan and intelligence to actually concieve and carry out such a design would be so far above us that it's actions and motives would be incomprehensible to us.

Irrelevant to the question of whether the universe was created or not. Of course, there is always the possibility that the ID would communicate with us and tell us what some of the actions and motivations were. Religions call this "revelation".

Because of the unknowns and the unknowables, I think debate on Intelligent Design falls into the category of "Philosophy" more than any other.

It can, but most of the unknowns and unknowables that you discuss are irrelevant to answering the 2 questions where direct actions by an IDer (deity) are hypothesized. We don't have to know exact identity or motives to answer the question. Instead, it's a matter of data. We simply don't have the data currently to answer the question.

I have certainly done my part in eating enough and resting enough to maintain my previous condition. So why has my body chosen to revert to my present condition? What advantage is my present lack of stamina relative to last fall?

Remember, we didn't evolve in a sedentary environment. Our hominid ancestors evolved with a very active lifestyle: foraging for food, avoiding predators, etc. Thus, we didn't really have downtime of resting when they were in Africa.

Muscle uses more energy and protein per unit mass than fat. Thus, when muscles are not exercised they do not maintain their mass. That uses less energy to replace the proteins that make up the muscle. In fat, once it's made, it just sits there and doesn't need replacement. But proteins are different. They are constantly being broken down and replaced by newly synthesized proteins. That synthesis takes energy.

In our ancestry, high caloric food was not nearly as abundant as it is today. So our ancestors adapted energy saving mechanisms -- and atrophy of muscles not in use was one of them. You have lots of food during the winter, but our H. sapiens ancestors in Europe during winter did not. They had to get by on very little when it was too cold and stormy to go out hunting/gathering. To "maintain" your muscle mass, you need to exercise, not just sit around.

So, life is here and already a ton of questions arise from this "little" fact.

All your questions relate to abiogenesis, not evolution.

The one way we know will generate life from non-living chemicals solves all your "problems".

http://www.theharbinger.org/articles/rel_sci/fox.html

http://www.siu.edu/~protocell/

If amino acids are heated -- either dry heated in an evaporating tidal pool or at underwater hydrothermal vents -- they polymerize to proteins. When water comes back into the tidal pool or the proteins are carried into cooler water, the proteins spontaneously form living cells (called protocells), each about the size of a bacterium.

1. You get tens of thousands to millions of protocells each time the reaction happens. That solves your problem of how many.

2. The protocells grow and reproduce. It's not a "plan" but chemistry. However, that solves your problem of death.

3. Protocells probably formed millions of different times. In fact, they are still forming now at hydrothermal vents. Of course, the protocells formed now are facing living organisms with 3.8 billion years of evolution behind them. So the modern organisms have the protocells for lunch. But this solves your problem of whether it was a one-time thing or many times. It also means that the protocells competed against each other for many millions of years and evolved until all the cells around were descended from just one of them -- the last common ancestor.

Higher pressure broadens the range that NH3 is liquid

http://www.daviddarling.info/encyclopedia/A/ammonialife.html

Good point Thank you for the information.

Boron based life might be more conducive to Ammonia as a solvent.

 

http://www.daviddarling.info/encyclopedia/B/boron-based_life.html

However, as the author notes, boron has other problems: "One of the biggest drawbacks to boron as a basis for life it is [sic] scarcity. On Earth, its abundance in the continental crust is only about 10 parts per million, so that any biology would seem to depend on their being present some mechanism for bringing about greater local concentrations of the element."

Another drawback is that boron apparently doesn't make polymers. It's difficult to imagine life without polymers to act as catalysts or hereditary material.

So, while boron might work well with ammonia as a solvent, the other drawbacks would seem to limit its utility as a basis for life.

I know someone with freckles.

So do I. My father had them all over his body. If you read the website I posted, you find that freckles result from concentrations of granules of pheomelanin.

I don't think I'd read it. I'm already familiar with evolution and the Origin is outdated,

Most of Origin is not outdated. The basic 5 theories that Darwin proposes in Origin are still valid today. And data does not get outdated. I think you, in particular, would benefit from the definition of natural selection at the end of Chapter IV.

But protein synthesis requires a lot of nucleic-acid transcription and translation of genetic code. You’d need a living cell with a genetic code, a transcription/translation system, and a few ribosomes to get the proteins you need.

Directed protein synthesis in modern cells requires all this, but protein synthesis does not. You can get the proteins you "need" by thermal polymerization of amino acids. Once you have proteins, some of those proteins will synthesize other proteins as long as there are amino acids present (which you need for directed protein synthesis too).

Sorry, lucaspa, but this is NOT the same thing as synthesizing life from scratch.

Did you read the websites? Why isn't it abiogenesis? This isn't either of the examples you cited. You start with amino acids. Heat them dry or at a simulated hydrothermal vent. The heating causes the amino acids to polymerize to proteins. Then add water. The proteins spontaneously turn into cells. Those cells (called protocells):

1. Metabolize (both anabolism and catabolism)

2. Respond to stimuli (have action potentials like nerve cells)

3. Grow

4. Reproduce

Those are the 4 activities that define what is "alive". So, explain why this isn't abiogenesis. It's not a "nice collection of spare nucleotides or mail-order genes".

I happen to be an untheist: one who believes that it doesn't matter if there is or isn't a god.

ROFL! You just made that up, didn't you? Nobody but creationists argue so strongly against abiogenesis. According to you, it matters very much if there is a god. Without one, you claim there is no way to get life! So your whole arguments here contradict your own position as a non-theist!

In The Profound Mystery Of Life3, We have discussed in detail why water is of great importance for life.

Good grief! You can find a discussion of the importance of water for life in any biochemistry text! The biochemistry text I had 37 years ago did this!

To interpret that water is one of the physical environment for life’s evolvement, we must prove that water had formed first, and then the organic substance of life came formed on the earth。

Been done. Evidence of sedimentary rocks and water erosion of basaltic rocks predates the earliest fossils of life found.

Origin of life? Here's one way:

http://www.theharbinger.org/articles/rel_sci/fox.html

http://www.siu.edu/~protocell/

Alright, but "doing best in the struggle for existence" is necessarily defined by having the most and/or most successful offspring, right?

That is going to be the result, not the definition. Having more offspring, and thus changing the allele frequency in the next generation, gives us an objective way to determine who was doing better. But the goal of natural selection is to adapt the population to a particular environment or, IOW, find the best designs available for that environment.

It seems like you could flip it around and call that the goal, in which case preserving the best designs would be the side effect. Which I guess is one reason why it's pointless to talk about "goals" at all, since there aren't any.

Having more offspring itself is not a "goal". If it were, every species would produce a huge number of offspring, but they don't. Salmon and sturgeon produce massive numbers of offspring -- tens of thousands per breeding pair -- but only because that is the design that allows survival in the struggle for existence. Other species produce few offspring but give them a lot of parental care, because that design does better in the struggle for existence in their environment.

The "goal" of natural selection is to produce the best design available for that particular environment. Which is exactly the "goal" in artificial selection and genetic algorithms. The only difference is that humans set the environment.

I'm sure it would yield something that can solve problems and interact convincingly with humans, but it seems like it would almost certainly end up doing those things in ways quite differently than human brains do. Or am I just totally off base?

Probably. After all, there are usually several designs that will give the same overall function in nature. It's called convergent evolution. BUT, the question was about producing artificial intelligence comparable to human intelligence, wasn't it? It wasn't about producing intelligence in exactly the same way that human brains do.

Altho, if the circuits were in a neural network, the way that the machine produced intelligence would be very close to how the human brain does it.

EDIT: How about modelling an actual human brain as closely as possible, and applying evolutionary algorithms to that model? (Is that what we've been talking about all along?)

That would be 1) unnecessarily restrictive for a non-biological machine and 2) undoable at the present, since we don' know how the human brain does things. There are still several different theories out there on how the brain does thinking. A SciAm article in the last 2 years discussed 2 of the theories.

No, we have not been talking about modelling the human brain. The biological connections are not exactly like the circuits on chips. Restricting AI research this way would be counter-productive. Better to set the environment and let natural selection find a way for the machine to get there instead of limiting it to just one path.

Firstly, let’s define “evolution” in the Darwinian sense: It means “decent with modification,” arising from the Malthusian principle that more offspring are produced by a population than can be sustained by its habitat (or environment).

With all respect, you are confusing different parts of evolution. Yes, evolution is "descent with modification". One method of modification is natural selection. Part of what makes natural selection wor is the more offspring are produced by a population than can be supported by the environment. So you have attached a part of natural selection as part of the definition of evolution.

Secondly, lets’ define “natural selection” in the Darwinian sense: It means an occurrence of differential reproductive success amongst the individuals of a population. That’s all it is.

No, it's not. Here's where people need to read Darwin. If you are going to "define natural selection in the Darwinian sense", then you must use Darwin's definition of natural selection!

So, let's put up Darwin's definition:

"If, during the long course of ages and under varying conditions of life, organic beings vary at all in the several parts of their organization, and I think this cannot be disputed; if there be, owing to the high geometric powers of increase of each species, at some age, season, or year, a severe struggle for life, and this certainly cannot be disputed; then, considering the infinite complexity of the relations of all organic beings to each other and to their conditions of existence, causing an infinite diversity in structure, constitution, and habits, to be advantageous to them, I think it would be a most extraordinary fact if no variation ever had occurred useful to each beings welfare, in the same way as so many variations have occured useful to man. But if variations useful to any organic being do occur, assuredly individuals thus characterized will have the best chance of being preserved in the struggle for life; and from the strong principle of inheritance they will will tend to produce offspring similarly characterized. This principle of preservation, I have called, for the sake of brevity, Natural Selection." [Origin, p 127 6th ed.]

Now we can easily see that differential reproductive success is secondary. It's a result of natural selection. The primary focus of natural selection is the production of designs in living organisms. Natural selection is an unintelligent process for producing designs.

Darwin deliberately used "selection" because "natural selection" was the artificial selection used by human breeders happening in nature. But you can see that Darwin emphasized preservation, not "elimination". The variations eliminated are not important, what is important are the variations preserved.

A portion of a population might be crushed by falling rocks, and we might be more accurate to call it NE than NS, because rocks can eliminate but they can’t select.

This is different. This is called "nonselective mortality". Being crushed by a rock does nothing to preserve the individual in the struggle for existence. Having quick reflexes to avoid the rocks in an area prone to frequent earthquakes is a trait that would be selected.

There are five “drivers,” if you will, of neo-Darwinian evolution, or decent with modification at the genomic level:

 

1. genetic mutation—digital disruptions of genetic code

2. gene flow—digit code moving laterally from one genome to another

3. Random genetic drift—bottlenecking and the founder effect

4. Sexual selection—preferential mating

5. Natural selection—differential reproductive success.

Congratulations on re-inventing the wheel! Have you ever heard of Hardy-Weinberg? That principle, based in Mendelian genetics, states that the frequency of an allele in a large population will remain the same from generation to generation unless affected by outside influences. What you did was list the 5 things that will disturb a Hardy-Weinberg equilibrium.

BUT, the only one of those that will produce the designs we see in plants and animals is natural selection.

Instead of trying to confuse yourself and others, I suggest you just do a bit of elemental reading about evolution. I suggest Evolutionary Biology by Douglas Futuyma.

BTW, gene flow is not "digit code moving laterally from one genome to another" but rather individuals from outside the population mating with individuals within the population. "digit code moving laterally from one genome to another" is "lateral gene transfer" in microorganisms.

Is it just me or is there anything that doesn't need water to live? why is life so attracted to water?

It's not that life is attracted to water, but rather that water has unique properties as a liquid that are conducive to life. I suggest getting hold of a biochemistry textbook. They all have several pages devoted to the role water plays in living organisms.

The only other liquid that has comparable properties to water would be liquid ammonia. Unfortunately, ammonia is only a liquid at < -33°C, which is too cold for the reactions that are life to proceed quickly enough.

Wondered if anyone has any thoughts on this, and particular whether any biologists who've read it think it's worth doing so.

Does a biochemist count? I've read it and found it very worth doing. What people don't realize is that there is a lot of data in Origin. More importantly, many of Darwin's ideas have become distorted in the popular mind. IMO, Darwin' summary of natural selection is a must read for everyone, since it dispels many of the misconceptions out there about what natural selection is. Another must read is the diagram (yes, there's only one). It illustrates perfectly that higher taxa are simply multiple speciation events spread thru time. So, if you have speciation, then you have all of evolution.

The style, of course, is difficult. Darwin was a clear writer, for his time. Times change and we now find much of the writing horribly stilted. But it's still worth the time reading Origin. If you ever discuss evolution with creationists, it's mandatory. All creationist arguments are simply recycled ones, and Origin provides refutation to all of them.

I assume a designed algorithm would be quite different from natural selection, though. For one thing, the "goal" would be different. With natural selection, the "goal" is always passing on genes to successful offspring as many times as possible.

The "goal" of natural selection is not "passing on genes to successful offspring". That's a result of the goal. The "goal" of natural selection is to preserve the designs that do best in the struggle for existence in that particular environment.

So "designed algorithms" are recreations of natural selection. What they do is set the environment and then natural selection finds designs that do well in that environment. For AI research, the "environment" would be cognitive problem solving and social skills (just as it was for hominids during evolution). Together that might produce the ability to "think" in a machine.

More trivially, there would also be much less time between generations, and less randomness (in nature, the individual can only have a better chance of survival based on genetics, but its still just a chance).

Randomness would be the same or a bit larger in genetic algorithms. After all, there is only so much change you can make in a protein and still have it function. Here, the ability to change circuits would be greater.

Yes, an individual might be killed by something unrelated to its new design (adaptation). This is called "nonselective mortality". But in the long run in nature that is moot. Populations still evolve even if 99% of mortality is nonselective.

"Thus much, perhaps most, of the mortality suffered by a population may be random with respect to this locus or character [hoofs in horses, for example] These nonselective deaths may be contrasted with selective death, those that contribute to the difference in fitness between genotypes. Even if most mortality is nonselective, the selective deaths that do occur can be a potent source of natural selection. For instance, genetic differences in swimming speed in a small planktonic crustacean might well not affect the likelihood of being eaten by baleen whales, which might be the major source of mortality. But if swimming speed affects escape from another predator species, even one that accounts for only 1 percent of the deaths, there will be an average difference in fitness, and swimming speed may evolve by natural selection." Futuyma, Evolutionary Biology, pg 368.

I've placed your text back in this post, and I'll have to re-create my reply later, and reply to this. It might be a few days, though - I've got all-day animal surgery tomorrow.

Thanks. And no problem on the wait. I've got a paper to submit tomorrow. But since it's going to take you a while, consider this also before you reply.

In the second edition of Principia, Newton listed 4 "rules of reasoning in philosophy" Look at #1:

"We are to admit no more causes of natural things than such as are both true and sufficient to explain their appearance". This, to me, sounds more like what you say is "Ockham's Razor" than what William of Ockham stated.

I will now quote from John Losee's A Historical Introduction to the Philosophy of Science, 4th edition, pg 83-84.

"In support of Rule 1, Newton appealed to a principle of parsimony, declaing that nature "affects not the pomp of superfluous causes". But exactly what Newton meant, or should have meant, by a "true cause" has beena subject of some debate. For instance, both William Whewell and John Stuart Mill criticized Newton for failing to specify criteria for the indentification of true causes. Whewell remarked that if Newton meant to restrict the "true cause" of a type of phenomnea to causes already known to be effective in producing other types of phenomena, then Rule 1 would be overly restrictive. It would preclude the introduction of new causes. However, Whewell was not certain that this was Newton's intended meaning. He noted that Newton may have meant only to restrict the introduction of causes to those of "similar in kind" to causes that previously have been established. Whewell observed that, thus interpreted, Rule 1 would be too vague to guide scientific inquiry. Any hypothetical cause could be claimed to display some similarity to previously established causes. Having dismissed these inadequate alternatives, Whewell suggested that what Newton should have meant by "true cause" is a cause represented in a theory, which theory is supported by inductive evidence acquired from analysis of diverse types of phenomenon.

Mill likewise interpreted "true cause" so as to reflect his own philosophical position. Consistent with his view of induction as a theory of proof of causal connection, Mill maintained that what disntinguishes a "true cause" is that its connection with the effect ascribed to it be susceptible to proof by independent evidence."

I would note that the term "sufficient" is being ignored by Losee. What generally accepted criteria do we have that a cause is "sufficient"? Within the limited area of being a material cause, we may have such criteria. But extended to a general idea of "sufficiency", there is a failure of consensus on criteria.

All in all, Rule 1 does not work as a means of theory evaluation. I would note that science has discarded Rule 3:

"In experimental philosophy we are to look upon propositions inferred by general induction from phenomena as accuarately or very nearly true, notwithstanding any contrary hypothesis that may be imagined, till such time as other phenomena occur, by which they may either be made more accurate, or liable to exceptions."

IOW, by Newton's rule, we can't falsify theories! Instead, data that contradicts them simply is viewed as exceptions to the theory.