Open questions in biology, biochemistry, and evolution
https://reasonandscience.catsboard.com/t2299-open-questions-in-biology-biochemistry-and-evolution
God is an ever-receding pocket of scientific ignorance
Neil de Grasse
Naturalism is an ever-receding pocket of scientific ignorance
Otangelo Grasso
When methodological naturalism is applied, the only explanation for the origin of life is abiogenesis, and of biodiversity, Darwins Theory of evolution. Proponents repeat like a mantra: Evolution is a fact. If that were the case, there would exist far more convincing, clear scientific answers to almost all relevant scientific questions and issues. This is far from being the case. Based on scientific papers, quite a different picture arises. Instead of compelling answers, question marks and lack of understanding, generalized ignorance in regard of almost all relevant issues, and conceptual problems are the most common. Since the information is widely sparse and scattered amongst thousands of scientific papers, it's not so evident that this is the factual state of matter. The general public is duped by effect slogans, that give the false impression of certainty of naturalism. The standard answer, when proponents of naturalism are confronted with this situation, is: "We are working on it". Or: "We don't know yet".
As if naturalism would be the answer in the future, no matter what. Aren't these not a prima facie of " evolution of the gaps" arguments? The question is: If a certain line of reasoning is not persuasive or convincing, or only leads to dead ends, then why do proponents of materialism not change their mind because of it? The more scientific papers are published, the less likely the scenario of evolution and abiogenesis and cosmic evolution becomes. The gaps are NOT being closed. They widen more and more. Some evolutionary predictions have even been falsified. We should consider the fact that modern biology may have reached its limits on several key issues and subjects. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios, or in a confession of ignorance. Fact is there remains a huge gulf in our understanding This lack of understanding is not just ignorance about some secondary details; it is a big conceptual gap. The reach of the end of the road is evident in the matter of almost all major questions.
The major questions of evolutionary novelties and abiogenesis are very far from being clearly formulated, even understood, and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be found. It doesn't take a couple of months, and a new scientific paper with wild speculations about abiogenesis is published, and eagerly swallowed by the anxious public, that finally wants its preferred worldview being confirmed. We don't know yet, therefore evolution and abiogenesis? That way, the design hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence does not provide satisfactory explanations through naturalism, why should we not change your minds and look somewhere else? I see only one reason: there is a emotional commitment to naturalism. Reason is not on the side of the materialist. The believer in creation IMHO has good reasons to hold his worldview. Reason is on his side. The evidence points massively in that direction. There is certainly the opponent just right on the corner, eagerly waiting to claim " argument of ignorance ". Because evolution is not true, intelligent design is ?! I suggest to read the answer here: http://reasonandscience.heavenforum.org/t1983-is-irreducible-complexity-merely-an-argument-from-ignorance?highlight=ignorance
Biological evolution has not brought us the slightest understanding of how the first living organisms emerged from inanimate matter on this planet and how the advanced eukaryotic cells—the highly structured building blocks of advanced life forms—ever emerged from simpler organisms. Neither does it explain one of the greatest mysteries of science: how did consciousness arise in living things? Where do symbolic thinking and self-awareness come from? 36
If naturalistic explanations of the origin of life are not convincing, why not look somewhere else ?
http://reasonandscience.heavenforum.org/t1508-will-we-eventually-discover-a-naturalistic-explanation-for-first-life
If a certain line of reasoning is not persuasive or convincing, then why do atheists not change their mind because of it? The more evolution papers are published, the less likely the scenario becomes. Some assertions have even been falsified. We should consider the fact that modern biology may have reached its limits on several subjects of biology. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios, or in a confession of ignorance. Fact is there remains a huge gulf in our understanding… This lack of understanding is not just ignorance about some technical details; it is a big conceptual gap. The reach of the end of the road is evident in the matter of almost all major questions. The major questions of macro change and abiogenesis are very far from being clearly formulated, even understood, and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be on sight. Isn't that a prima facie of a " evolution of the gap" argument ? We don't know yet, therefore evolution and abiogenesis ? That way, the God hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence does not provide satisfactory explanations through naturalism, why should we not change your minds and look somewhere else ?
Following a list of open questions and unanswered problems:
Origin and evolution of the genetic code: the universal enigma 1
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
Modern cells possess a sophisticated metabolic network, but its origins remain largely unknown. 2
Some of the remaining questions associated with it appear, however, to be the most crucial ones. First, how did early biomolecules, supposedly nucleotides, sugars, amino acids and fatty acids, form and reach life compatible concentrations? In this context, one needs to consider how the first forms of geochemical carbon fixation could have taken place [3,4]. Moreover, as life is unlikely to have started in an extreme dilute solution, this suggests that it was, from the beginning, bound by some sort of compartmentalization [5,6]. 32
Cells use sophisticated regulation to transform static genomic information into flexible function. We are still far from understanding how such regulation evolves. 3
Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii
The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. 4
Spinach, Or The Search For The Secret Of Life As We Know It
Deep in the heart of this nest of proteins lies the manganese cluster, whose precise arrangement of atoms remains one of biology's outstanding problems. 5
Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers
One of the outstanding questions concerning the early Earth is how ancient phototrophs made the evolutionary transition from anoxygenic to oxygenic photosynthesis, which resulted in a substantial increase in the amount of oxygen in the atmosphere. 6
TRANSITION TO OXYGENIC PHOTOSYNTHESIS
Perhaps the most widely discussed yet poorly understood event in the evolution of photosynthesis is the invention of the ability to use water as an electron donor, producing O2 as a waste product and giving rise to what is now called oxygenic photosynthesis. 7
Complex evolution of photosynthesis
The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits 8
The Continuing Puzzle of the Great Oxidation Event
While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved. The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown. 9
Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. 10
Origin and evolution of metabolic pathway
How the major metabolic pathways actually originated is still an open question, but several different theories have been suggested to account for the establishment of metabolic routes All these ideas are based on gene duplication. 11
The Evolution of Electron-Transport Chains
How did the crucial individual components—ATP synthase, redox-driven H+ pumps, and photosystems—first arise? Hypotheses about events occurring on an evolutionary time scale are difficult to test. 12
Early Fixation of an Optimal Genetic Code
The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. 13
Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. 14
Basic functional states in the evolution of light-driven cyclic electron transport
It's a difficult problem for evolutionary theory, to say the least. How, within the available time, and by known mechanisms, did the necessary bacterial proteins arise? "From the data presented," concluded Scherer, "the evolution of cyclic photosynthetic electron transport is an unsolved problem in theoretical biology. On the basis of present understanding, no solution can be expected." 15
Proponents of evolution since have freely admitted that the origin of gender and sexual reproduction still remains one of the most difficult problems in biology 17
Evolutionary Origin of Recombination during Meiosis
The origin of meiosis, and in particular meiotic recombina-tion, is an unresolved mystery in biology
Evolution of Human Language Still a Mystery
“This kind of straightforward connection is just not the way organisms are put together,” he says. When it comes to something as complex as language, “one would be hard-pressed to come up with an example less amenable to evolutionary study.” And the specific Foxp2 connection is based on a whole chain of events, each of which is speculative, so there’s little chance of the whole story being right. 18
"The Integration Hypothesis of Human Language Evolution and Its Implications for the Study of Contemporary Languages"
How human language arose is a great mystery in the evolution of Homo sapiens. 19
Locomotion: The Case for a Designer
Why did vertebrates evolve two additional muscle types? Do we have animals or fossils that demonstrate this transition? The evolutionary theory is unable to answer these questions. 20
Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes
The evolutionary origin of centriole/kinetosomes, centrosomes, and other microtubule organizing centers (MTOCs), whether by direct filiation or symbiogenesis, has been controversial for >50 years. 21
On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. 22
Genome-wide analysis reveals origin of transfer RNA genes from tRNA halves.
Transfer RNAs (tRNAs) play an important role linking mitochondrial RNA and amino acids during protein biogenesis. Four types of tRNA genes have been identified in living organisms. However, the evolutionary origin of tRNAs remains largely unknown 23
Evolution of the Lyrebird
Although there is evidence that females choose the males with the most complexity and accuracy in their voice, it remains unclear why these traits would be appealing as evolutionary selection.
Absurd Creature of the Week: This Fish Swims Up a Sea Cucumber’s Butt and Eats Its Gonads
And it’s important to consider that the fish in fact benefits from the evisceration, because by using the sea cucumber as a home, it necessarily adopts its host’s predators. Its survival depends on the sea cucumber’s ability to defend itself, which is quite intriguing from an evolutionary perspective. 24
Absurd Creature of the Week: This Shrew Can Survive You Standing on It (Maybe. Please Don’t Try)
According to Stanley, its spine is, relative to body size, four times more robust than that of any other vertebrate, which poses quite the evolutionary conundrum: This is a singular species whose backbone is miles away from its shrew cousins. There’s a more typical shrew at one extreme and then the hero shrew at the other, with no species in between. This might suggest that the evolution of the robust spine was supremely rapid and dramatic, an evolutionary principle known as punctuated equilibrium, because there are no intermediate forms between the two to indicate a more gradual development. 25
Bioenergetics and Life's Origins
A plausible energy source for polymerization remains an open question. Condensation reactions driven by cycles of anhydrous conditions and hydration would seem to be one obvious possibility, but seem limited by the lack of specificity of the chemical bonds that are formed. 27
I would have thought a bigger question was what drives the relationship between brain evolution and body evolution. I would not expect a single genetic mutation to affect both the brain and body.......so what causes a sequence of mutations to converge in such a manner that the brain evolves to match the body functionality and vice versa. Surely for every permanent genetic change there have to be TWO mutations at a time ( one for body, one for brain ) in a long succession of such mutations. How, for example, does a primitive bird's brain know that the creature has developed wings ? 28
Evolution of sex and recombination: data
In summary, much of our work points to coevolutionary interactions with parasites as a mechanism selecting for sexual reproduction over parthenogenesis. There, nonetheless, remain important theoretical (link to theory) and empirical difficulties. For example, critical details regarding the genetic basis of infection have yet to be worked out. 29
How did sex start?
The areas discussed below pose the most profound challenges to evolutionary science. Despite years of research and discussion (and, in some cases, promising directions), there are still no answers. Origin of Sex. Why is sexuality so widespread in nature? How did this maleness and femaleness arise? If it is necessary to maintain genetic variability, why can many microorganisms do without it? How can one account for such phenomena as parthenogenesis: frog eggs, for instance, can produce tadpoles if they are pricked by pins or stimulated by electric current, without having been fertilized by male sperm. 30
Most of the single-celled organisms in the world, like bacteria, reproduce asexually by making copies of themselves. So how did sex come to rule the animal kingdom? Scientists have been trying to figure out the origin of sex for hundreds of years, without much luck.
Asexual reproduction is more convenient and requires less effort: there’s no search for a partner and you get to pass all your genes along, from the U.K.’s National History Museum:
In many ways asexual reproduction is the better evolutionary strategy: only one parent is needed and all of their genes are passed on to the next generation. All bacteria, most plants and even some animals reproduce asexually at least some of the time.
Sex is less efficient. Finding a mate can take time and energy, and any gametes that aren’t fertilised go to waste. Plus, each parent only passes half of its genes to the offspring.
Origin of Life. How did living matter originate out of nonliving matter? Was it a process that happened once or many times? Can it still happen today under natural or artificial conditions? Did it evolve out of the kind of growth and replication processes we see in crystals or on an entirely different basis?
Origin of Sex. Why is sexuality so widespread in nature? How did this maleness and femaleness arise? If it is necessary to maintain genetic variability, why can many microorganisms do without it? How can one account for such phenomena as parthenogenesis: frog eggs, for instance, can produce tadpoles if they are pricked by pins or stimulated by electric current, without having been fertilized by male sperm.
Origin of Language. How did human speech originate? We see no examples of primitive languages on Earth today; all mankind’s languages are evolved and complex. Can the answer be sought in the structure of the brain, experiments on teaching apes, animal communication systems or is there no way to ever find out?
Origin of Phyla. What is the evolutionary relationship between existing phyla and those of the past? There is still no agreement on how many there are today, how many we know from the fossil past and which may have come out of which. Transitional forms between phyla are almost unknown.
Cause of Mass Extinctions. Asteroids are currently in vogue, but far from proven as a cause of world-wide extinctions. And though punctuated equilibrium theory helps account for the so-called sudden appearance of new groups, and long persistence of others, it has raised many new questions about stability and extinction of species.
Relationship between DNA and Phenotype. Can small steady changes (micromutations) account for evolution, or must there be periodic larger jumps (macromutations)? Is DNA a complete blueprint for the individual, or is it subject to various influences and constraints in its expression? Are there any circumstances under which environment or behavior can work “backwards,” influencing changes in DNA?
How Much Can Natural Selection Explain? Darwin never claimed natural selection is the only mechanism of evolution. Although he considered it a major explanation, he continued to search for others, and the search continues.
Early Evolution of Photosynthesis 31
Evolutionary origins of oxygen evolution center and linked photosystems are important unsolved problems.
To understand the origin and early evolution of photosynthesis, we need to consider mechanisms and evolution of all these subsystems and processes:
Pigments ( Chls , carotenoids, bilins )
Reaction centers (including O2 Evolution Center)
Antenna complexes
Electron transfer pathways
Carbon fixation pathways
Photoprotection mechanisms
Integration into cellular metabolism
No single branching diagram can represent the complex path of evolution of photosynthesis.
The evolution of PS2 proteins has been partially by gene recruitment and partially by gene duplication, but most of the proteins are orphans, with no known source.
Origin and Evolution of Photosynthesis- Remaining Challenges
Nature of the earliest PS systems not known
Significance of gene duplications in RC evolution not understood
Evolutionary origin of the oxygen evolving complex not known
No good understanding of how two photosystems were linked in series
Theoretical physicist and mathematician Freeman Dyson, “How We Know,” New York Review of Books, March 10, 2011.
“THE PUBLIC HAS A DISTORTED VIEW OF SCIENCE, BECAUSE CHILDREN ARE TAUGHT IN SCHOOL THAT SCIENCE IS A COLLECTION OF FIRMLY ESTABLISHED TRUTHS. IN FACT, SCIENCE IS NOT A COLLECTION OF TRUTHS. IT IS A CONTINUING EXPLORATION OF MYSTERIES. WHEREVER WE GO EXPLORING IN THE WORLD AROUND US, WE FIND MYSTERIES. OUR PLANET IS COVERED BY CONTINENTS AND OCEANS WHOSE ORIGIN WE CANNOT EXPLAIN. OUR ATMOSPHERE IS CONSTANTLY STIRRED BY POORLY UNDERSTOOD DISTURBANCES THAT WE CALL WEATHER AND CLIMATE. THE VISIBLE MATTER IN THE UNIVERSE IS OUTWEIGHED BY A MUCH LARGER QUANTITY OF DARK INVISIBLE MATTER THAT WE DO NOT UNDERSTAND AT ALL. THE ORIGIN OF LIFE IS A TOTAL MYSTERY, AND SO IS THE EXISTENCE OF HUMAN CONSCIOUSNESS. WE HAVE NO CLEAR IDEA HOW THE ELECTRICAL DISCHARGES OCCURRING IN NERVE CELLS IN OUR BRAINS ARE CONNECTED WITH OUR FEELINGS AND DESIRES AND ACTIONS EVEN PHYSICS, THE MOST EXACT AND MOST FIRMLY ESTABLISHED BRANCH OF SCIENCE,IS STILL FULL OF MYSTERIES.”
The origin and cellular complexity of eukaryotes represent a major enigma in biology. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. 33
The evolution of the network of non-equilibrium redox reactions that came to be the primary energy-transforming pathways of life on Earth remains largely unknown. 34
The iron metabolism is thought to be quite ancient but the evolution of the systems involved is largely unknown. 35
1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/
2) http://msb.embopress.org/content/10/4/725
3) http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0040007
4) http://www.nature.com/ncomms/2013/131106/ncomms3742/abs/ncomms3742.html?message-global=remove
5) http://newscenter.lbl.gov/2004/07/14/spinach-or-the-search-for-the-secret-of-life-as-we-know-it/
6) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289370/
7) http://www.nc bi.nlm.nih.gov/pmc/articles/PMC238882/
8 http://www.ncbi.nlm.nih.gov/pubmed/12221987
9) http://www.pnas.org/content/early/2013/06/20/1305530110
10)http://msb.embopress.org/content/10/4/725
11) http://flipper.diff.org/app/pathways/info/3461
12) http://www.ncbi.nlm.nih.gov/books/NBK26849/
13) http://mbe.oxfordjournals.org/content/17/4/511.long
14) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023395/
15) http://www.sciencedirect.com/science/article/pii/0022519383904162
16) http://www.goodreads.com/quotes/360178-the-public-has-a-distorted-view-of-science-because-children
17) http://www.trueorigin.org/sex01.php
18) http://www.redorbit.com/news/science/1258209/evolution_of_human_language_still_a_mystery/#I6ov7uxY5ams5hHB.99
19) http://www.lsa.umich.edu/vgn-ext-templating/v/index.jsp?vgnextoid=05fc5c8014082410VgnVCM100000c2b1d38dRCRD&vgnextchannel=715be32f33073310VgnVCM100000c2b1d38dRCRD&vgnextfmt=detail
20) http://www.apologeticspress.org/ApPubPage.aspx?pub=1&issue=581&article=625
21) http://www.pnas.org/content/early/2008/05/02/0802293105.abstract
22) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181368/
23) http://www.ncbi.nlm.nih.gov/pubmed/23744908
24) http://www.wired.com/2014/02/absurd-creature-of-the-week-pearlfish/
25) http://www.wired.com/2013/11/absurd-creature-of-the-week/
26) http://alumni.kcl.ac.uk/evolution-of-teeth
27) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828274/
28) http://old.richarddawkins.net/discussions/588704-what-is-the-the-big-unanswered-question-in-evolutionary-theory/comments?page=1
29) http://www.indiana.edu/~curtweb/Research/sex&recomb.html
30) http://www.ridgenet.net/~do_while/sage/v8i12f.htm
31) http://www.plantphysiol.org/content/154/2/434.full
32) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128644/
33) http://www.nature.com.ololo.sci-hub.cc/nature/journal/v541/n7637/full/nature21031.html
34) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2606772/#fn2
35) http://www.sciencedirect.com.https.sci-hub.hk/science/article/pii/S0005272812010407
https://reasonandscience.catsboard.com/t2299-open-questions-in-biology-biochemistry-and-evolution
God is an ever-receding pocket of scientific ignorance
Neil de Grasse
Naturalism is an ever-receding pocket of scientific ignorance
Otangelo Grasso
When methodological naturalism is applied, the only explanation for the origin of life is abiogenesis, and of biodiversity, Darwins Theory of evolution. Proponents repeat like a mantra: Evolution is a fact. If that were the case, there would exist far more convincing, clear scientific answers to almost all relevant scientific questions and issues. This is far from being the case. Based on scientific papers, quite a different picture arises. Instead of compelling answers, question marks and lack of understanding, generalized ignorance in regard of almost all relevant issues, and conceptual problems are the most common. Since the information is widely sparse and scattered amongst thousands of scientific papers, it's not so evident that this is the factual state of matter. The general public is duped by effect slogans, that give the false impression of certainty of naturalism. The standard answer, when proponents of naturalism are confronted with this situation, is: "We are working on it". Or: "We don't know yet".
As if naturalism would be the answer in the future, no matter what. Aren't these not a prima facie of " evolution of the gaps" arguments? The question is: If a certain line of reasoning is not persuasive or convincing, or only leads to dead ends, then why do proponents of materialism not change their mind because of it? The more scientific papers are published, the less likely the scenario of evolution and abiogenesis and cosmic evolution becomes. The gaps are NOT being closed. They widen more and more. Some evolutionary predictions have even been falsified. We should consider the fact that modern biology may have reached its limits on several key issues and subjects. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios, or in a confession of ignorance. Fact is there remains a huge gulf in our understanding This lack of understanding is not just ignorance about some secondary details; it is a big conceptual gap. The reach of the end of the road is evident in the matter of almost all major questions.
The major questions of evolutionary novelties and abiogenesis are very far from being clearly formulated, even understood, and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be found. It doesn't take a couple of months, and a new scientific paper with wild speculations about abiogenesis is published, and eagerly swallowed by the anxious public, that finally wants its preferred worldview being confirmed. We don't know yet, therefore evolution and abiogenesis? That way, the design hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence does not provide satisfactory explanations through naturalism, why should we not change your minds and look somewhere else? I see only one reason: there is a emotional commitment to naturalism. Reason is not on the side of the materialist. The believer in creation IMHO has good reasons to hold his worldview. Reason is on his side. The evidence points massively in that direction. There is certainly the opponent just right on the corner, eagerly waiting to claim " argument of ignorance ". Because evolution is not true, intelligent design is ?! I suggest to read the answer here: http://reasonandscience.heavenforum.org/t1983-is-irreducible-complexity-merely-an-argument-from-ignorance?highlight=ignorance
Biological evolution has not brought us the slightest understanding of how the first living organisms emerged from inanimate matter on this planet and how the advanced eukaryotic cells—the highly structured building blocks of advanced life forms—ever emerged from simpler organisms. Neither does it explain one of the greatest mysteries of science: how did consciousness arise in living things? Where do symbolic thinking and self-awareness come from? 36
If naturalistic explanations of the origin of life are not convincing, why not look somewhere else ?
http://reasonandscience.heavenforum.org/t1508-will-we-eventually-discover-a-naturalistic-explanation-for-first-life
If a certain line of reasoning is not persuasive or convincing, then why do atheists not change their mind because of it? The more evolution papers are published, the less likely the scenario becomes. Some assertions have even been falsified. We should consider the fact that modern biology may have reached its limits on several subjects of biology. All discussions on principal theories and experiments in the field either end in vague suppositions and guesswork, statements of blind faith, made up scenarios, or in a confession of ignorance. Fact is there remains a huge gulf in our understanding… This lack of understanding is not just ignorance about some technical details; it is a big conceptual gap. The reach of the end of the road is evident in the matter of almost all major questions. The major questions of macro change and abiogenesis are very far from being clearly formulated, even understood, and nowhere near being solved, and for most, there is no solution at all at sight. But proponents of evolution firmly believe, one day a solution will be on sight. Isn't that a prima facie of a " evolution of the gap" argument ? We don't know yet, therefore evolution and abiogenesis ? That way, the God hypothesis remains out of the equation in the beginning, and out at the end, and never receives a serious and honest consideration. If the scientific evidence does not provide satisfactory explanations through naturalism, why should we not change your minds and look somewhere else ?
Following a list of open questions and unanswered problems:
Origin and evolution of the genetic code: the universal enigma 1
In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made. Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.
Modern cells possess a sophisticated metabolic network, but its origins remain largely unknown. 2
Some of the remaining questions associated with it appear, however, to be the most crucial ones. First, how did early biomolecules, supposedly nucleotides, sugars, amino acids and fatty acids, form and reach life compatible concentrations? In this context, one needs to consider how the first forms of geochemical carbon fixation could have taken place [3,4]. Moreover, as life is unlikely to have started in an extreme dilute solution, this suggests that it was, from the beginning, bound by some sort of compartmentalization [5,6]. 32
Cells use sophisticated regulation to transform static genomic information into flexible function. We are still far from understanding how such regulation evolves. 3
Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii
The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. 4
Spinach, Or The Search For The Secret Of Life As We Know It
Deep in the heart of this nest of proteins lies the manganese cluster, whose precise arrangement of atoms remains one of biology's outstanding problems. 5
Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers
One of the outstanding questions concerning the early Earth is how ancient phototrophs made the evolutionary transition from anoxygenic to oxygenic photosynthesis, which resulted in a substantial increase in the amount of oxygen in the atmosphere. 6
TRANSITION TO OXYGENIC PHOTOSYNTHESIS
Perhaps the most widely discussed yet poorly understood event in the evolution of photosynthesis is the invention of the ability to use water as an electron donor, producing O2 as a waste product and giving rise to what is now called oxygenic photosynthesis. 7
Complex evolution of photosynthesis
The evolutionary path of type I and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits 8
The Continuing Puzzle of the Great Oxidation Event
While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved. The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown. 9
Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. 10
Origin and evolution of metabolic pathway
How the major metabolic pathways actually originated is still an open question, but several different theories have been suggested to account for the establishment of metabolic routes All these ideas are based on gene duplication. 11
The Evolution of Electron-Transport Chains
How did the crucial individual components—ATP synthase, redox-driven H+ pumps, and photosystems—first arise? Hypotheses about events occurring on an evolutionary time scale are difficult to test. 12
Early Fixation of an Optimal Genetic Code
The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. 13
Non‐enzymatic glycolysis and pentose phosphate pathway‐like reactions in a plausible Archean ocean
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. 14
Basic functional states in the evolution of light-driven cyclic electron transport
It's a difficult problem for evolutionary theory, to say the least. How, within the available time, and by known mechanisms, did the necessary bacterial proteins arise? "From the data presented," concluded Scherer, "the evolution of cyclic photosynthetic electron transport is an unsolved problem in theoretical biology. On the basis of present understanding, no solution can be expected." 15
Evolutionary Theories On Gender And Sexual Reproduction
Evolutionary Origin of Recombination during Meiosis
The origin of meiosis, and in particular meiotic recombina-tion, is an unresolved mystery in biology
Evolution of Human Language Still a Mystery
“This kind of straightforward connection is just not the way organisms are put together,” he says. When it comes to something as complex as language, “one would be hard-pressed to come up with an example less amenable to evolutionary study.” And the specific Foxp2 connection is based on a whole chain of events, each of which is speculative, so there’s little chance of the whole story being right. 18
"The Integration Hypothesis of Human Language Evolution and Its Implications for the Study of Contemporary Languages"
How human language arose is a great mystery in the evolution of Homo sapiens. 19
Locomotion: The Case for a Designer
Why did vertebrates evolve two additional muscle types? Do we have animals or fossils that demonstrate this transition? The evolutionary theory is unable to answer these questions. 20
Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes
The evolutionary origin of centriole/kinetosomes, centrosomes, and other microtubule organizing centers (MTOCs), whether by direct filiation or symbiogenesis, has been controversial for >50 years. 21
On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. 22
Genome-wide analysis reveals origin of transfer RNA genes from tRNA halves.
Transfer RNAs (tRNAs) play an important role linking mitochondrial RNA and amino acids during protein biogenesis. Four types of tRNA genes have been identified in living organisms. However, the evolutionary origin of tRNAs remains largely unknown 23
Evolution of the Lyrebird
Although there is evidence that females choose the males with the most complexity and accuracy in their voice, it remains unclear why these traits would be appealing as evolutionary selection.
Absurd Creature of the Week: This Fish Swims Up a Sea Cucumber’s Butt and Eats Its Gonads
And it’s important to consider that the fish in fact benefits from the evisceration, because by using the sea cucumber as a home, it necessarily adopts its host’s predators. Its survival depends on the sea cucumber’s ability to defend itself, which is quite intriguing from an evolutionary perspective. 24
Absurd Creature of the Week: This Shrew Can Survive You Standing on It (Maybe. Please Don’t Try)
According to Stanley, its spine is, relative to body size, four times more robust than that of any other vertebrate, which poses quite the evolutionary conundrum: This is a singular species whose backbone is miles away from its shrew cousins. There’s a more typical shrew at one extreme and then the hero shrew at the other, with no species in between. This might suggest that the evolution of the robust spine was supremely rapid and dramatic, an evolutionary principle known as punctuated equilibrium, because there are no intermediate forms between the two to indicate a more gradual development. 25
How did teeth evolve in our earliest ancestors?
Every jawed vertebrate needs teeth to function and feed. But exactly how teeth evolved is poorly understood, because it is difficult to interpret different stages of tooth development from fossils.Lead researcher Professor Moya Meredith Smith, Dental Institute at King’s, said: ‘We still don’t have a clear understanding of how dentitions are built. 26Bioenergetics and Life's Origins
A plausible energy source for polymerization remains an open question. Condensation reactions driven by cycles of anhydrous conditions and hydration would seem to be one obvious possibility, but seem limited by the lack of specificity of the chemical bonds that are formed. 27
I would have thought a bigger question was what drives the relationship between brain evolution and body evolution. I would not expect a single genetic mutation to affect both the brain and body.......so what causes a sequence of mutations to converge in such a manner that the brain evolves to match the body functionality and vice versa. Surely for every permanent genetic change there have to be TWO mutations at a time ( one for body, one for brain ) in a long succession of such mutations. How, for example, does a primitive bird's brain know that the creature has developed wings ? 28
Evolution of sex and recombination: data
In summary, much of our work points to coevolutionary interactions with parasites as a mechanism selecting for sexual reproduction over parthenogenesis. There, nonetheless, remain important theoretical (link to theory) and empirical difficulties. For example, critical details regarding the genetic basis of infection have yet to be worked out. 29
How did sex start?
The areas discussed below pose the most profound challenges to evolutionary science. Despite years of research and discussion (and, in some cases, promising directions), there are still no answers. Origin of Sex. Why is sexuality so widespread in nature? How did this maleness and femaleness arise? If it is necessary to maintain genetic variability, why can many microorganisms do without it? How can one account for such phenomena as parthenogenesis: frog eggs, for instance, can produce tadpoles if they are pricked by pins or stimulated by electric current, without having been fertilized by male sperm. 30
Most of the single-celled organisms in the world, like bacteria, reproduce asexually by making copies of themselves. So how did sex come to rule the animal kingdom? Scientists have been trying to figure out the origin of sex for hundreds of years, without much luck.
Asexual reproduction is more convenient and requires less effort: there’s no search for a partner and you get to pass all your genes along, from the U.K.’s National History Museum:
In many ways asexual reproduction is the better evolutionary strategy: only one parent is needed and all of their genes are passed on to the next generation. All bacteria, most plants and even some animals reproduce asexually at least some of the time.
Sex is less efficient. Finding a mate can take time and energy, and any gametes that aren’t fertilised go to waste. Plus, each parent only passes half of its genes to the offspring.
Origin of Life. How did living matter originate out of nonliving matter? Was it a process that happened once or many times? Can it still happen today under natural or artificial conditions? Did it evolve out of the kind of growth and replication processes we see in crystals or on an entirely different basis?
Origin of Sex. Why is sexuality so widespread in nature? How did this maleness and femaleness arise? If it is necessary to maintain genetic variability, why can many microorganisms do without it? How can one account for such phenomena as parthenogenesis: frog eggs, for instance, can produce tadpoles if they are pricked by pins or stimulated by electric current, without having been fertilized by male sperm.
Origin of Language. How did human speech originate? We see no examples of primitive languages on Earth today; all mankind’s languages are evolved and complex. Can the answer be sought in the structure of the brain, experiments on teaching apes, animal communication systems or is there no way to ever find out?
Origin of Phyla. What is the evolutionary relationship between existing phyla and those of the past? There is still no agreement on how many there are today, how many we know from the fossil past and which may have come out of which. Transitional forms between phyla are almost unknown.
Cause of Mass Extinctions. Asteroids are currently in vogue, but far from proven as a cause of world-wide extinctions. And though punctuated equilibrium theory helps account for the so-called sudden appearance of new groups, and long persistence of others, it has raised many new questions about stability and extinction of species.
Relationship between DNA and Phenotype. Can small steady changes (micromutations) account for evolution, or must there be periodic larger jumps (macromutations)? Is DNA a complete blueprint for the individual, or is it subject to various influences and constraints in its expression? Are there any circumstances under which environment or behavior can work “backwards,” influencing changes in DNA?
How Much Can Natural Selection Explain? Darwin never claimed natural selection is the only mechanism of evolution. Although he considered it a major explanation, he continued to search for others, and the search continues.
Early Evolution of Photosynthesis 31
Evolutionary origins of oxygen evolution center and linked photosystems are important unsolved problems.
To understand the origin and early evolution of photosynthesis, we need to consider mechanisms and evolution of all these subsystems and processes:
Pigments ( Chls , carotenoids, bilins )
Reaction centers (including O2 Evolution Center)
Antenna complexes
Electron transfer pathways
Carbon fixation pathways
Photoprotection mechanisms
Integration into cellular metabolism
No single branching diagram can represent the complex path of evolution of photosynthesis.
The evolution of PS2 proteins has been partially by gene recruitment and partially by gene duplication, but most of the proteins are orphans, with no known source.
Origin and Evolution of Photosynthesis- Remaining Challenges
Nature of the earliest PS systems not known
Significance of gene duplications in RC evolution not understood
Evolutionary origin of the oxygen evolving complex not known
No good understanding of how two photosystems were linked in series
Theoretical physicist and mathematician Freeman Dyson, “How We Know,” New York Review of Books, March 10, 2011.
“THE PUBLIC HAS A DISTORTED VIEW OF SCIENCE, BECAUSE CHILDREN ARE TAUGHT IN SCHOOL THAT SCIENCE IS A COLLECTION OF FIRMLY ESTABLISHED TRUTHS. IN FACT, SCIENCE IS NOT A COLLECTION OF TRUTHS. IT IS A CONTINUING EXPLORATION OF MYSTERIES. WHEREVER WE GO EXPLORING IN THE WORLD AROUND US, WE FIND MYSTERIES. OUR PLANET IS COVERED BY CONTINENTS AND OCEANS WHOSE ORIGIN WE CANNOT EXPLAIN. OUR ATMOSPHERE IS CONSTANTLY STIRRED BY POORLY UNDERSTOOD DISTURBANCES THAT WE CALL WEATHER AND CLIMATE. THE VISIBLE MATTER IN THE UNIVERSE IS OUTWEIGHED BY A MUCH LARGER QUANTITY OF DARK INVISIBLE MATTER THAT WE DO NOT UNDERSTAND AT ALL. THE ORIGIN OF LIFE IS A TOTAL MYSTERY, AND SO IS THE EXISTENCE OF HUMAN CONSCIOUSNESS. WE HAVE NO CLEAR IDEA HOW THE ELECTRICAL DISCHARGES OCCURRING IN NERVE CELLS IN OUR BRAINS ARE CONNECTED WITH OUR FEELINGS AND DESIRES AND ACTIONS EVEN PHYSICS, THE MOST EXACT AND MOST FIRMLY ESTABLISHED BRANCH OF SCIENCE,IS STILL FULL OF MYSTERIES.”
The origin and cellular complexity of eukaryotes represent a major enigma in biology. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. 33
The evolution of the network of non-equilibrium redox reactions that came to be the primary energy-transforming pathways of life on Earth remains largely unknown. 34
The iron metabolism is thought to be quite ancient but the evolution of the systems involved is largely unknown. 35
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2) http://msb.embopress.org/content/10/4/725
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14) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4023395/
15) http://www.sciencedirect.com/science/article/pii/0022519383904162
16) http://www.goodreads.com/quotes/360178-the-public-has-a-distorted-view-of-science-because-children
17) http://www.trueorigin.org/sex01.php
18) http://www.redorbit.com/news/science/1258209/evolution_of_human_language_still_a_mystery/#I6ov7uxY5ams5hHB.99
19) http://www.lsa.umich.edu/vgn-ext-templating/v/index.jsp?vgnextoid=05fc5c8014082410VgnVCM100000c2b1d38dRCRD&vgnextchannel=715be32f33073310VgnVCM100000c2b1d38dRCRD&vgnextfmt=detail
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21) http://www.pnas.org/content/early/2008/05/02/0802293105.abstract
22) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181368/
23) http://www.ncbi.nlm.nih.gov/pubmed/23744908
24) http://www.wired.com/2014/02/absurd-creature-of-the-week-pearlfish/
25) http://www.wired.com/2013/11/absurd-creature-of-the-week/
26) http://alumni.kcl.ac.uk/evolution-of-teeth
27) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828274/
28) http://old.richarddawkins.net/discussions/588704-what-is-the-the-big-unanswered-question-in-evolutionary-theory/comments?page=1
29) http://www.indiana.edu/~curtweb/Research/sex&recomb.html
30) http://www.ridgenet.net/~do_while/sage/v8i12f.htm
31) http://www.plantphysiol.org/content/154/2/434.full
32) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128644/
33) http://www.nature.com.ololo.sci-hub.cc/nature/journal/v541/n7637/full/nature21031.html
34) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2606772/#fn2
35) http://www.sciencedirect.com.https.sci-hub.hk/science/article/pii/S0005272812010407
Last edited by Admin on Sat Nov 24, 2018 4:07 am; edited 19 times in total
