The evolution of the brain and nervous system, and the mind and consciousness

[shunyadragon]

New research reveals details of the first steps of the evolution of the nervous system:

Before nerves, there were peptides | Cosmos

Before nerves, there were peptides
Researchers map communication pathways in an organism that has no nervous system. Nick Carne reports.

Placozoans reacting to peptides.

UNIVERSITY OF EXETER
Animal nervous systems evolved from much more simple structures in part because of a novel form of communication, according to new research.

An international team of scientists has found that simple multicellular organisms called Placozoa can coordinate their movement and body shape in the absence of a nervous system by signalling between cells using short chains of amino acids known as peptides.

That’s significant because it echoes how more complex organisms use similar structures, known as neuropeptides, for signalling within the nervous system.

“It might seem strange to use an animal with no neurons or synapses to study nervous system evolution, but although Placozoans are nerveless, you can still find within their cells the basic molecules needed for communication in complex nervous systems,” says Frédérique Varoqueaux, from the University of Lausanne in Switzerland.

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“So studying Placozoans can tell us more about the origins of neurons and how they became the body's control system.”

The organisms are just one millimetre in size and look like tiny hairy discs. Although they have only three cell layers and no true nerve or muscle cells, they glide across surfaces in the ocean with apparent ease.

The new study found that their cells contain a variety of small peptides, made up of between four and 20 amino acids that are secreted from one cell and detected by neighbouring ones.

Experiments revealed that the peptides changed Placozoan behaviour within seconds. Each had a unique effect, which in some cases was very dramatic. The main changes included crinkling, turning, flattening, and internal churning, a behaviour associated with feeding.

“Each peptide can be used individually as a different signal, but the peptides could also be used sequentially or together in different combinations which allows for very high numbers of unique signals between cells,” says Gáspár Jékely from the University of Exeter in the UK.

“This explains how Placozoans can coordinate sophisticated behavioural sequences such as feeding."

 

[Salvador]

A precursory human-like mind and consciousness evolved when a couple of Australopithecus hetero zygotes, who had the same type of chromosome rearrangements formed by fusion of the whole long arms of two acrocentric chromosomes, mated together and reproduced viable and fertile offspring with 46 chromosomes. This first generation of Homo habilis then may have likely incestuously bred with each other and reproduced the next subsequent generation of Homo habilis.

Unfortunately, this hypothesis is neither falsifiable nor verifiable since an Australophithecus brain and DNA specimen can't be obtained for comparison with a Homo habilis brain and DNA specimen.

 

[shunyadragon]

A precursory human-like mind and consciousness evolved when a couple of Australopithecus hetero zygotes, who had the same type of chromosome rearrangements formed by fusion of the whole long arms of two acrocentric chromosomes, mated together and reproduced viable and fertile offspring with 46 chromosomes. This first generation of Homo habilis then may have likely incestuously bred with each other and reproduced the next subsequent generation of Homo habilis.

Unfortunately, this hypothesis is neither falsifiable nor verifiable since an Australophithecus brain and DNA specimen can't be obtained for comparison with a Homo habilis brain and DNA specimen.

'Arguing from ignorance' cannot get you a cup of coffee for a three dollar bill.

 

[Salvador]

'Arguing from ignorance' cannot get you a cup of coffee for a three dollar bill.

I have lots of hypothesis that seem to me to be very plausible but are not yet testable with current technological limitations ;, it's not my fault I live in an era where we know so little of the conditions and details of what happened billions or even just millions of years ago, so then, that doesn't necessarily make me ignorant. Who knows? Maybe with future technology to enable further scientific exploration, many of the hypothesis I strongly believe to be proven true will either be validated or falsified.

 

[shunyadragon]

I have lots of hypothesis that seem to me to be very plausible but are not yet testable with current technological limitations ;, it's not my fault I live in an era where we know so little of the conditions and details of what happened billions or even just millions of years ago, so then, that doesn't necessarily make me ignorant. Who knows? Maybe with future technology to enable further scientific exploration, many of the hypothesis I strongly believe to be proven true will either be validated or falsified.

First, hypothesis are not proven. Second, like I stated before the highlighted above is classic 'arguing from ignorance.' I did not say you were ignorant. I was referring to the fallacy.

Arguing from the perspective of what you believe that science 'does not know' is an argument from ignorance.'

The science of the genetics of evolution in this case you cite is more involved than your simplistic description. You made the assertion of what 'science cannot falsify,' which is a conclusive statement as to what science can and cannot, this is not science. Pick one facet of the argument of the brain does not an argument make.

 

[gnostic]

I have lots of hypothesis that seem to me to be very plausible but are not yet testable with current technological limitations ;, it's not my fault I live in an era where we know so little of the conditions and details of what happened billions or even just millions of years ago, so then, that doesn't necessarily make me ignorant. Who knows? Maybe with future technology to enable further scientific exploration, many of the hypothesis I strongly believe to be proven true will either be validated or falsified.

I really don’t think you understand what “hypothesis” mean, in the scientific context.

As used in science, hypotheses don’t mean any made up claims or made up stories.

There are requirements and restrictions to what can be called “hypothesis” (as used in science), just as there are requirements and restrictions to what is a “scientific theory”.

All creationists and some theists that don’t have science background, don’t understand what is hypothesis and what is scientific theory, and confused with these two terms with everyday uses of these words.

As I said, hypothesis as used in science, have specific requirements that must be met, so here is definition of what a hypothesis is:

A hypothesis is set of explanations and predictions made from or based on preliminary observation, and that hypothesis must meet the requirements of being “falsifiable”.

But what do “falsifiable” actually mean in scientific context?

Falsifiable mean that any statement made are REFUTABLE, meaning the statement have to the potential of being “tested”, hence falsifiable means the hypothesis must be “TESTABLE”.

Being testable, mean (A) evidences can be discovered, or (B) that you can perform experiments based on the hypothesis’ parameters, repeatedly.

If the claim isn’t falsifiable, then it mean you cannot test it, and if you cannot test it, then the claim isn’t a “hypothesis”.

God or gods “isn’t testable”, hence “unfalsifiable”. Spirits, soul, ghosts, angels, demons, jinns, fairies, ghoul and goblin, miracles, magic, afterlife, resurrection, reincarnation, heaven and hell, and anything “supernatural” are all considered “untestable”, therefore “unfalsifiable”.

Any unfalsifiable claim are not only “not hypothesis”, but are pseudoscience and baseless fantasies or superstitions.

Intelligent Design isn’t a hypothesis, because the concept of the “Designer”, like that of “Creator” or “God”, isn’t testable or isn’t falsifiable.

Michael Behe’s Irreducible Complexity is a bunch of claims that relied on circular reasonings, not testable evidences. All he is doing is rationalizing that because of complexity of DNA or other biological organs, for instances, therefore intelligent entity is required “to design them”, is merely a baseless word game and useless and faulty anecdotes of design requiring designer.

Behe like everyone else at the Discovery Institute are merely using propaganda to promote their beliefs.

Science required more than just logic and anecdotes; science required ample empirical and testable evidences.

 

[gnostic]

Oops, I have accidentally press the “Post Reply” button.

I was going to talk more about hypothesis, how scientists don’t set out “prove” or “disprove” hypothesis, because proving or disproving relates to “proof”, not testable evidence.

Proof is a logical statement often represented in the forms of mathematical equations or formulas, or as a mathematical model.

I was going to explain the differences between proof and evidence, and they don’t mean the same things in science.

And I was going to explain what theoretical science is, and how theoretical physicists and their models rely more on maths (hence proofs, eg mathematical models) than on evidences.

 

[Salvador]

I really don’t think you understand what “hypothesis” mean, in the scientific context.

As used in science, hypotheses don’t mean any made up claims or made up stories.

There are requirements and restrictions to what can be called “hypothesis” (as used in science), just as there are requirements and restrictions to what is a “scientific theory”.

All creationists and some theists that don’t have science background, don’t understand what is hypothesis and what is scientific theory, and confused with these two terms with everyday uses of these words.

As I said, hypothesis as used in science, have specific requirements that must be met, so here is definition of what a hypothesis is:

A hypothesis is set of explanations and predictions made from or based on preliminary observation, and that hypothesis must meet the requirements of being “falsifiable”.

But what do “falsifiable” actually mean in scientific context?

Falsifiable mean that any statement made are REFUTABLE, meaning the statement have to the potential of being “tested”, hence falsifiable means the hypothesis must be “TESTABLE”.

Being testable, mean (A) evidences can be discovered, or (B) that you can perform experiments based on the hypothesis’ parameters, repeatedly.

If the claim isn’t falsifiable, then it mean you cannot test it, and if you cannot test it, then the claim isn’t a “hypothesis”.

God or gods “isn’t testable”, hence “unfalsifiable”. Spirits, soul, ghosts, angels, demons, jinns, fairies, ghoul and goblin, miracles, magic, afterlife, resurrection, reincarnation, heaven and hell, and anything “supernatural” are all considered “untestable”, therefore “unfalsifiable”.

Any unfalsifiable claim are not only “not hypothesis”, but are pseudoscience and baseless fantasies or superstitions.

Intelligent Design isn’t a hypothesis, because the concept of the “Designer”, like that of “Creator” or “God”, isn’t testable or isn’t falsifiable.

Michael Behe’s Irreducible Complexity is a bunch of claims that relied on circular reasonings, not testable evidences. All he is doing is rationalizing that because of complexity of DNA or other biological organs, for instances, therefore intelligent entity is required “to design them”, is merely a baseless word game and useless and faulty anecdotes of design requiring designer.

Behe like everyone else at the Discovery Institute are merely using propaganda to promote their beliefs.

Science required more than just logic and anecdotes; science required ample empirical and testable evidences.

There is in fact empirical evidence for a mark of intelligence left in our genetic code as evident by how the numeric and semantic message of 037 appears in our genetic code. Each codon relates to 3 other particular codons having the same particular type of initial nucleobase and sequential nucleobase subsequently then followed by a different ending nucleobase. Half of these 4 set of codon groups ( whole family codons ) each code for the same particular amino acid. The other half of those 4 set of codon groups ( split codons ) don't code for the same amino acid. So then, in the case of whole family codons, there are 37 amino acid peptide chain nucleons for each relevant nucleobase determinant of how a particular amino acid gets coded. Start codons express 0 at the beginning of 37 Hence, the meaningful numeric and semantic message of 037 gets unambiguously and factually conveyed to us descendants of our cosmic ancestor(s) with our genetic code invented by a superior intelligence beyond that of anybody presently bound to Earth.

“There is no plausible chemical logic to couple directly the triplets and the amino acids. In other words, the principles of chemistry where not the sought essence of the genetic code”

“The zero is the supreme abstraction of arithmetic. Its use by any alphabet, including the genetic code, can be an indicator of artificiality.”

"The place-value decimal system represented through digital symmetry of the numbers divisible by prime number (PN 037). This arithmetical syntactic feature is an innate attribute of the genetic code. The PN 037 notation with a leading zero emphasizes zero's equal participation in the digital symmetry. Numbers written by identical digits are devised by PN 037*3=111 and 1+1+1=3 and appear regularly [from the figure: 037*6 =222 and 2+2+2=6, 037*9=333 and 3+3+3 =9, 037*4=444 and 4+4+4=12, 037*15=555 and 5+5+5=15, 037*18=666 and 6+6+6=18, 037*21=777 and 7+7+7 =21. 037*24 =888 and 8+8+8=24, 037*27=999 and 9+9+9=27.)"

"There is a complete set of information symbols utilizing the decimal syntax 111, 222, 333, 444, 555, 666, 777, 888, 999 in the genetic code. Each of these symbols consists uniformly of a carrier (balanced nucleons) and a meaning (the decimal syntax)."

Reference: The "Wow! signal" of the terrestrial genetic code. Vladimir l. shCherbak and Maxim A. Makukov. Redirectinghttps://www.scribd.com/document/35302916...netic-Code

"The first information system emerged on the earth as primordial version of the genetic code and genetic texts. The natural appearance of arithmetic power in such a linguistic milieu is theoretically possible and practical for producing information systems of extremely high efficiency. In this case, the arithmetic symbols should be incorporated into an alphabet, i.e. the genetic code. A number is the fundamental arithmetic symbol produced by the system of numeration. If the system of numeration were detected inside the genetic code, it would be natural to expect that its purpose is arithmetic calculation e.g., for the sake of control, safety, and precise alteration of the genetic texts. The nucleons of amino acids and the bases of nucleic acids seem most suitable for embodiments of digits. These assumptions were used for the analyzing the genetic code.

The compressed, life-size, and split representation of the Escherichia coli and Euplotes octocarinatus code versions were considered simultaneously. An exact equilibration of the nucleon sums of the amino acid standard blocks and/or side chains was found repeatedly within specified sets of the genetic code. Moreover, the digital notations of the balanced sums acquired, in decimal representation, the unique form 111, 222, …, 999. This form is a consequence of the criterion of divisibility by 037. The criterion could simplify some computing mechanism of a cell if any and facilitate its computational procedure.

Reference: Biosystems Volume 70, Issue 3, August 2003, Pages 187-209
"Arithmetic inside the universal genetic code" Author: Vladimir I. shCherbak
https://www.sciencedirect.com/science/ar...4703000662

"Numerous arithmetical regularities of nucleon numbers of canonical amino acids for quite different systematizations of the genetic code, which are dominantly based on decimal number 037, indicate the hidden existence of a more universal ordering principle. Mathematical analysis of number 037 reveals that it is a unique decimal number from which an infinite set of self-similar numbers can be derived with the nested numerical, geometrical, and arithmetical properties, thus enabling the nested coding and computing in the (bio)systems by geometry and resonance. The omnipresent fractal structural and dynamical organization, as well as the intertwining of quantum and classical realm in the physical and biological systems could be just the consequence of such coding and computing."

Reference: NeuroQuantology | December 2011 | Vol 9 | Issue 4 | Page 702-715 Masic, Natasa Nested Properties of shCherbak’s PQ 037 and (Biological) Coding/Computing Nested Numeric/Geometric/Arithmetic Propertiesof shCherbak’s Prime Quantum 037 as a Base of (Biological) Coding/Computing
http://Nested Numeric/Geometric/Arithmetic Properties

 

[tas8831]

A precursory human-like mind and consciousness evolved when a couple of Australopithecus hetero zygotes, who had the same type of chromosome rearrangements formed by fusion of the whole long arms of two acrocentric chromosomes, mated together and reproduced viable and fertile offspring with 46 chromosomes. This first generation of Homo habilis then may have likely incestuously bred with each other and reproduced the next subsequent generation of Homo habilis.

It seems more likely that the chromosome fusion took place after the split from the lineage leading to chimps and had nothing to do with the actual speciation event, since there does not appear to be any genetic disruptions as a result of the fusion (at least as of the last I read up on the subject).

In addition, the alteration of the karyotype is not in and of itself an enigma, regarding having to mate with another member of the same species of the opposite sex already possessing the anomaly since there are many example of extant mammalian taxa that have and even maintain karytotypic polymorphisms.

 

[tas8831]

There is in fact empirical evidence for a mark of intelligence left in our genetic code as evident by how the numeric and semantic message of 037 appears in our genetic code.

I find all of this sort of 'amazing discoveries' to be on par with the amazing Bible Code hysteria of a decade or so ago. You only get the amazing outcomes if you apply the parameters used by the 'discoverers'. I recall reading that someone had used an alteration of the bible code folks and found the 'hidden' message of 'Darwin was right' in the bible.

Also, I am no mathematician, but I did do some googling about this whole 037 issue, and I came across a few rebuttals at various places, to include a snarky response that more or less summarizes my take on these sorts of papers, regardless of who wrote them, from "Graham" at the forum 'Pharyngula':

If you look through a pack of cards, you will be able to find coincidences and patterns. Perhaps all four queens occur together. Perhaps the last ten cards all correspond to prime numbers. The more ingenious you are in the way you look, and the more open you are to different kinds of patterns, the more you will see. The more work you put in, the more you can get out. More formally, the greater the information content of the extraction process, the greater the information content of the result.

Suppose someone decides to throw out the black cards, and just look for patterns among the red ones. It might seem they have just made one choice - red vs black. You could formalize this by saying they have put one bit of information into the extraction process. You would be wrong. They have actually made several choices: They've decided to throw out some cards. (Why? Surely it is more natural to look at them all together? And if we're allowed to throw some out, why not add cards according to some scheme? You could cut the red ones in half for example, to make two red cards for each old one.) Secondly, they've decided to use colour as the criterion for choosing which cards to chuck, when cards have other attributes that could just as well have been used.

It is not possible to evaluate things like this rigourously. You may feel that throwing out some cards is a fairly reasonable thing to do, while cutting some in half is highly contrived. You might then assign just a a couple of bits to a decision to throw, and quite a lot of bits to a decision to cut. Someone else might disagree with your numbers. At any rate, it is crucial to consider all the things you might reasonably have done but didn't, when evaluating a process for extracting patterns. Otherwise, you might unwittingly put more information into the extraction process than you get out as a 'message'.

Bear these considerations in mind when reading the following list of decisions which are used to extract meaning from the genetic code in the paper. There are two major phases: converting (codon,amino acid) pairs to numbers, then looking for patterns in the numbers.

Primary Phase: Making Numbers

1. Decide to throw out the codons and focus on just the amino acids.

2. Decide to map amino acids to numbers, in particular positive integers. Human mathematicians study many kinds of mathematical objects. Graphs, or groups, or sequences of numbers are other possibilities.

3. Decide to disregard the molecular structure of the amino acids and regard them as just an unordered bunch of atoms. There are many numbers that one could derive from the molecular structure using the elements and/or the types of chemical bonds present, or the underlying graph.

4. Decide to focus on the nucleus of the atoms, and ignore the numbers one might derive from the electron shells. (Surely it is a shame not to get a mention of quantum spin into a story like this. Everybody likes a bit of quantum spin.)

5. Decide to ignore the fundamental constituents of the nucleus (the quarks - at least as far we understand the nucleus) and instead focus on the protons and neutrons.

6. Decide to ignore the obvious positive integer related to an atom, that is, the atomic number, which is the number of protons, and also the number of electrons if the atom is not ionized, and instead decide to include the neutrons, despite the fact that this number varies with the isotope. We can choose the most common isotope, and call the result a 'nucleon sum'.

Secondary Phase: Spotting Patterns

7. There's all sorts of things one can do with numbers. Find their prime factors, interpret them as coefficients of a polynomial and look at the roots, interpret them as coefficients of a continued fraction, add them up, subtract them, multiply or divide, compare them to physical or chemical constants, or to numbers that seem important from mathematics, and so on. But we might decide to divide them into two subsets and add them up to form two subsums. Whatever.

8. We've got 20 numbers and there are over a million ways to divide them up, but some ways seem more natural given the genetic code. But wait! We could make more than 20 numbers (or indeed less since some of the numbers are the same). But let's decide to make a few more. Not all amino acids are coded equally. Some might need special treatment. Met and Trp are special, because they are associated with only one codon. Leu, Ser, and Arg are the only ones where the first two letters of the codon can vary. Ser is extraspecial because its codons are not all connected by single substitutions. Ile is special because it is the only one with 3 codons. And Tyr, Cys and Trp are special because their codon shares the first two letters with a Stop codon. And Stop codons are very special. And so on. Anyway, lets decide to make a few more numbers by splitting the Leu, Ser, and Arg numbers into two, according to the first two letters in their codons.

9. There are about 8 million ways to divide the now 23 numbers into two sets. The codons associated with them suggest various more or less contrived possibilities.

Results

For some of these possibilities, it turns out that both subsums are equal and divisible by 37, and 37 is half the nucleon sum of the B groups, apart from proline.

Interpretation

We apologise for the anti-climax.​

If the researchers had used slightly different parameters, their amazing miraculous find would not have been found. It is a product of number manipulation and pattern seeking, nothing more.

 

[tas8831]

I have read a bit about the original paper (oddly, published in an astrophysics journal) and am now even more dismissive of the results - at least one amino acid did not fit their chosen scheme, so they fiddled with its structure so that it would. I am betting this was not mentioned in any of the various youtube proclamations on the subject.

 

[Salvador]

I have read a bit about the original paper (oddly, published in an astrophysics journal) and am now even more dismissive of the results - at least one amino acid did not fit their chosen scheme, so they fiddled with its structure so that it would. I am betting this was not mentioned in any of the various youtube proclamations on the subject.

"All arithmetical patterns considered further appear with the differentiation between blocks and chains in 131 all 20 amino acids and with the subsequent transfer of one nucleon from side chain to block in proline 132 (Fig. 2b). Proline is the only exception from the general structure of amino acids: it holds its side chain 133 with two bonds and has one hydrogen less in its block. The mentioned transfer in proline “standardizes” its 134 block nucleon number to 73 + 1 and reduces its chain nucleons to 42 – 1. In itself, the distinction between 135 blocks and chains is purely formal: there is no stage in protein synthesis where amino acid side chains are 136 detached from standard blocks. Therefore, there is no any natural reason for nucleon transfer in proline; it 137 can be simulated only in the mind of a recipient to achieve the array of amino acids with uniform structure. 138 Such nucleon transfer thus appears artificial. However, exactly this seems to be its destination: it protects 139 the patterns from any natural explanation. Minimizing the chances for appealing to natural origin is a 140 distinct concern in messaging of such kind, and this problem seems to be solved perfectly for the signal in 141 the genetic code. Applied systematically without exceptions, the artificial transfer in proline enables 142 holistic and arithmetically precise order in the code. Thus, it acts as an “activation key”. While nature deals 143 with the actual proline which does not produce the signal in the code, an intelligent recipient easily finds 144 the key and reads messages in arithmetical language"

Reference: The “Wow! signal” of the terrestrial genetic code Authors: Vladimir I. shCherbak a , Maxim A. Makukov Icarus (2013) 2.4 The Activation Key

 

[Salvador]

I find all of this sort of 'amazing discoveries' to be on par with the amazing Bible Code hysteria of a decade or so ago. You only get the amazing outcomes if you apply the parameters used by the 'discoverers'. I recall reading that someone had used an alteration of the bible code folks and found the 'hidden' message of 'Darwin was right' in the bible.

Also, I am no mathematician, but I did do some googling about this whole 037 issue, and I came across a few rebuttals at various places, to include a snarky response that more or less summarizes my take on these sorts of papers, regardless of who wrote them, from "Graham" at the forum 'Pharyngula':

If you look through a pack of cards, you will be able to find coincidences and patterns. Perhaps all four queens occur together. Perhaps the last ten cards all correspond to prime numbers. The more ingenious you are in the way you look, and the more open you are to different kinds of patterns, the more you will see. The more work you put in, the more you can get out. More formally, the greater the information content of the extraction process, the greater the information content of the result.

Suppose someone decides to throw out the black cards, and just look for patterns among the red ones. It might seem they have just made one choice - red vs black. You could formalize this by saying they have put one bit of information into the extraction process. You would be wrong. They have actually made several choices: They've decided to throw out some cards. (Why? Surely it is more natural to look at them all together? And if we're allowed to throw some out, why not add cards according to some scheme? You could cut the red ones in half for example, to make two red cards for each old one.) Secondly, they've decided to use colour as the criterion for choosing which cards to chuck, when cards have other attributes that could just as well have been used.

It is not possible to evaluate things like this rigourously. You may feel that throwing out some cards is a fairly reasonable thing to do, while cutting some in half is highly contrived. You might then assign just a a couple of bits to a decision to throw, and quite a lot of bits to a decision to cut. Someone else might disagree with your numbers. At any rate, it is crucial to consider all the things you might reasonably have done but didn't, when evaluating a process for extracting patterns. Otherwise, you might unwittingly put more information into the extraction process than you get out as a 'message'.

Bear these considerations in mind when reading the following list of decisions which are used to extract meaning from the genetic code in the paper. There are two major phases: converting (codon,amino acid) pairs to numbers, then looking for patterns in the numbers.

Primary Phase: Making Numbers

1. Decide to throw out the codons and focus on just the amino acids.

2. Decide to map amino acids to numbers, in particular positive integers. Human mathematicians study many kinds of mathematical objects. Graphs, or groups, or sequences of numbers are other possibilities.

3. Decide to disregard the molecular structure of the amino acids and regard them as just an unordered bunch of atoms. There are many numbers that one could derive from the molecular structure using the elements and/or the types of chemical bonds present, or the underlying graph.

4. Decide to focus on the nucleus of the atoms, and ignore the numbers one might derive from the electron shells. (Surely it is a shame not to get a mention of quantum spin into a story like this. Everybody likes a bit of quantum spin.)

5. Decide to ignore the fundamental constituents of the nucleus (the quarks - at least as far we understand the nucleus) and instead focus on the protons and neutrons.

6. Decide to ignore the obvious positive integer related to an atom, that is, the atomic number, which is the number of protons, and also the number of electrons if the atom is not ionized, and instead decide to include the neutrons, despite the fact that this number varies with the isotope. We can choose the most common isotope, and call the result a 'nucleon sum'.

Secondary Phase: Spotting Patterns

7. There's all sorts of things one can do with numbers. Find their prime factors, interpret them as coefficients of a polynomial and look at the roots, interpret them as coefficients of a continued fraction, add them up, subtract them, multiply or divide, compare them to physical or chemical constants, or to numbers that seem important from mathematics, and so on. But we might decide to divide them into two subsets and add them up to form two subsums. Whatever.

8. We've got 20 numbers and there are over a million ways to divide them up, but some ways seem more natural given the genetic code. But wait! We could make more than 20 numbers (or indeed less since some of the numbers are the same). But let's decide to make a few more. Not all amino acids are coded equally. Some might need special treatment. Met and Trp are special, because they are associated with only one codon. Leu, Ser, and Arg are the only ones where the first two letters of the codon can vary. Ser is extraspecial because its codons are not all connected by single substitutions. Ile is special because it is the only one with 3 codons. And Tyr, Cys and Trp are special because their codon shares the first two letters with a Stop codon. And Stop codons are very special. And so on. Anyway, lets decide to make a few more numbers by splitting the Leu, Ser, and Arg numbers into two, according to the first two letters in their codons.

9. There are about 8 million ways to divide the now 23 numbers into two sets. The codons associated with them suggest various more or less contrived possibilities.

Results

For some of these possibilities, it turns out that both subsums are equal and divisible by 37, and 37 is half the nucleon sum of the B groups, apart from proline.

Interpretation

We apologise for the anti-climax.​

If the researchers had used slightly different parameters, their amazing miraculous find would not have been found. It is a product of number manipulation and pattern seeking, nothing more.

"".Hi, I'm one of the authors of the papers being discussed here (thanks for pointing out this discussion, Simone). Saying right off: I am not going to make war and press on changing anything in the wiki-article. I'll appreciate if the wiki-editors here will take my note into account; but if not - well, I can live with that, From the discussion here I see that the point is not whether our papers are ID or not (they are not; if that matters - I share entirely naturalistic worldview). Rather, the point is whether they are numerology or not. As I guess, this is a short way of saying that the data we described might be just the result of our arbitrary "juggling" until we found some "desired patterns". In our recent paper (mentioned here by the user Andy Shepp) we devote a good chunk of text to discussing this very point, so here I'll instead make a comparison between our study and the Bible Code (the comparison brought about by PZ Myers, I suppose). First - there is no any scientific hypothesis behind the Bible code (at least none that I've heard of. God? That's not a hypothesis, since the notion of God is notoriously ill-defined. Without such restriction, you are free to choose/invent any method you like for data analysis. In our case, we have the working hypothesis (that of Sagan and Crick & Orgel), and we attempt to develop analysis methodology appropriate for that hypothesis - the condition which greatly restricts the options (in particular, we are trying to follow similar basic logic that was used to construct Earth-made messages such as the Arecibo message, etc.). Second - the analogy with the Bible code is irrelevant simply from statistical standpoint. In one case the data (Bible) is millions of letters long - what a scope for opportunities. In another case, the data (genetic code) is only a few hundred bits. Next, the Bible is but one of many books ever written, while the genetic code is unique (with several minor variations). The Bible is written with a writing system which is itself completely arbitrary and is but one of many existing writing systems; in contrast, in our approach we do not rely in any way on arbitrary cultural codes, relying instead on the language of abstract logic and mathematics (yes, I know not everyone agrees that even mathematics might be useful for communication with another intelligent species; still, if you attempt to do that, first of all you'll most probalby resort to logic/mathematics, not Hebrew, right?). ----------- Of course, I by no means imply that our data unambiguously supports the hypothesis of Crick & Orgel. My point is that the data favors this hypothesis to the extent which makes it unreasonable to dismiss it as numerology just like the Bible code. As typically happens in such situations, the problem is that it is difficult to find an objective criterion for judging opinions and biases." - Maxim Makukov

Reference: Wikipedia Talk Panspermia Talkanspermia - Wikipedia

 

[shunyadragon]

"All arithmetical patterns considered further appear with the differentiation between blocks and chains in 131 all 20 amino acids and with the subsequent transfer of one nucleon from side chain to block in proline 132 (Fig. 2b). Proline is the only exception from the general structure of amino acids: it holds its side chain 133 with two bonds and has one hydrogen less in its block. The mentioned transfer in proline “standardizes” its 134 block nucleon number to 73 + 1 and reduces its chain nucleons to 42 – 1. In itself, the distinction between 135 blocks and chains is purely formal: there is no stage in protein synthesis where amino acid side chains are 136 detached from standard blocks. Therefore, there is no any natural reason for nucleon transfer in proline; it 137 can be simulated only in the mind of a recipient to achieve the array of amino acids with uniform structure. 138 Such nucleon transfer thus appears artificial. However, exactly this seems to be its destination: it protects 139 the patterns from any natural explanation. Minimizing the chances for appealing to natural origin is a 140 distinct concern in messaging of such kind, and this problem seems to be solved perfectly for the signal in 141 the genetic code. Applied systematically without exceptions, the artificial transfer in proline enables 142 holistic and arithmetically precise order in the code. Thus, it acts as an “activation key”. While nature deals 143 with the actual proline which does not produce the signal in the code, an intelligent recipient easily finds 144 the key and reads messages in arithmetical language"

Reference: The “Wow! signal” of the terrestrial genetic code Authors: Vladimir I. shCherbak a , Maxim A. Makukov Icarus (2013) 2.4 The Activation Key

More boggus manipulation with an agenda using ENRON bookkeeping math.

 

[Salvador]

It seems more likely that the chromosome fusion took place after the split from the lineage leading to chimps and had nothing to do with the actual speciation event, since there does not appear to be any genetic disruptions as a result of the fusion (at least as of the last I read up on the subject).

In addition, the alteration of the karyotype is not in and of itself an enigma, regarding having to mate with another member of the same species of the opposite sex already possessing the anomaly since there are many example of extant mammalian taxa that have and even maintain karytotypic polymorphisms.

The genomes of extinct species related directly to modern-day humans, such as Neanderthals and Denisovans indicate these species already possessed the chromosome fusion originating from the long chromosome 2 characteristic of homo sapiens

Reference:

1. Meyer et al. 2012 A high-coverage genome sequence from an archaic Denisovan individual. Science, 338:222-226.; K. H. Miga. 2016. Chromosome-specific Centromere sequences provide an estímate of the Ancestral Chromosome 2 Fusion event in Hominin Genome.Journ. of Heredity. 1-8. Doi:10.1093/jhered/esw039.

Thus, this rearrangement of chromosomes occurred an estimated 750,000 to 4,500,000 years ago.

Since Neanderthals and Denisovans had the same number of chromosome as modern-day humans do could explain why descendants from inter-species cross-breeding with homo sapiens were possibly fetile and viable. This explains why traces of their genetic characteristics remain in the human genome, as a comparative genomic analysis of the 3 species demonstrates. However, any hypothetical descendants from the breeding between Neanderthals, Denisovans and Homo-genus species (46 chromosomes) and their large ape ancestors (48 chromosomes) would have had problems of chromosome incompatibility and would have unlikely been viable. There are no traces of specific genetic characteristics of the large apes found in the human genome. So then, the chromosome fusion possibly acted as an efficient mechanism for reproductive isolation that isolated the ancestors of the large apes from homo-genus species.

Finally, there the possibility chromosome fusion originating with homo-genus specie's chromosome 2 might have been affiliated with the appearance of distinctive homo-genus specie traits. Therefore, several genes in homo-genus specie's chromosome 2 found close to the chromosome 2 fusion's region are expressed more intensely in homo sapiens than in that of large apes. These genes are expressed, above all, in highly significant organs and tissues, like the gonads and brains . Reference: GTEx Portal, http://www.gtexportal.org/home.

Furthermore, the loss of particular DNA sequences that happened from the fusion resulting in homo-genus specie's Chromosome 2 might have had “positive” effects on the ancestors of modern day humans.

In the near future, biologists hopefully will be able obtain the DNA of extinct species that are older than Homo Heidelbergensis/Homo Erectus, thereby determining if the Homo-genus specie's Chromosome 2 fusion is associated with all “human” lineages; Unfortunately, a complete comparative analysis of the fusion region of human chromosome 2 and the sub-telomeric regions of the 2 large ape chromosomes involved in this fusion is not currently possible.

 

[tas8831]

Interesting information - seems to support my contention, thanks.

The genomes of extinct species related directly to modern-day humans, such as Neanderthals and Denisovans indicate these species already possessed the chromosome fusion originating from the long chromosome 2 characteristic of homo sapiens

Reference:

1. Meyer et al. 2012 A high-coverage genome sequence from an archaic Denisovan individual. Science, 338:222-226.; K. H. Miga. 2016. Chromosome-specific Centromere sequences provide an estímate of the Ancestral Chromosome 2 Fusion event in Hominin Genome.Journ. of Heredity. 1-8. Doi:10.1093/jhered/esw039.

Thus, this rearrangement of chromosomes occurred an estimated 750,000 to 4,500,000 years ago.

Since Neanderthals and Denisovans had the same number of chromosome as modern-day humans do could explain why descendants from inter-species cross-breeding with homo sapiens were possibly fetile and viable. This explains why traces of their genetic characteristics remain in the human genome, as a comparative genomic analysis of the 3 species demonstrates. However, any hypothetical descendants from the breeding between Neanderthals, Denisovans and Homo-genus species (46 chromosomes) and their large ape ancestors (48 chromosomes) would have had problems of chromosome incompatibility and would have unlikely been viable. There are no traces of specific genetic characteristics of the large apes found in the human genome. So then, the chromosome fusion possibly acted as an efficient mechanism for reproductive isolation that isolated the ancestors of the large apes from homo-genus species.

Finally, there the possibility chromosome fusion originating with homo-genus specie's chromosome 2 might have been affiliated with the appearance of distinctive homo-genus specie traits. Therefore, several genes in homo-genus specie's chromosome 2 found close to the chromosome 2 fusion's region are expressed more intensely in homo sapiens than in that of large apes. These genes are expressed, above all, in highly significant organs and tissues, like the gonads and brains . Reference: GTEx Portal, http://www.gtexportal.org/home.

Furthermore, the loss of particular DNA sequences that happened from the fusion resulting in homo-genus specie's Chromosome 2 might have had “positive” effects on the ancestors of modern day humans.

In the near future, biologists hopefully will be able obtain the DNA of extinct species that are older than Homo Heidelbergensis/Homo Erectus, thereby determining if the Homo-genus specie's Chromosome 2 fusion is associated with all “human” lineages; Unfortunately, a complete comparative analysis of the fusion region of human chromosome 2 and the sub-telomeric regions of the 2 large ape chromosomes involved in this fusion is not currently possible.

 

[sealchan]

New research reveals details of the first steps of the evolution of the nervous system:

Before nerves, there were peptides | Cosmos

Before nerves, there were peptides
Researchers map communication pathways in an organism that has no nervous system. Nick Carne reports.

Placozoans reacting to peptides.

UNIVERSITY OF EXETER
Animal nervous systems evolved from much more simple structures in part because of a novel form of communication, according to new research.

An international team of scientists has found that simple multicellular organisms called Placozoa can coordinate their movement and body shape in the absence of a nervous system by signalling between cells using short chains of amino acids known as peptides.

That’s significant because it echoes how more complex organisms use similar structures, known as neuropeptides, for signalling within the nervous system.

“It might seem strange to use an animal with no neurons or synapses to study nervous system evolution, but although Placozoans are nerveless, you can still find within their cells the basic molecules needed for communication in complex nervous systems,” says Frédérique Varoqueaux, from the University of Lausanne in Switzerland.

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“So studying Placozoans can tell us more about the origins of neurons and how they became the body's control system.”

The organisms are just one millimetre in size and look like tiny hairy discs. Although they have only three cell layers and no true nerve or muscle cells, they glide across surfaces in the ocean with apparent ease.

The new study found that their cells contain a variety of small peptides, made up of between four and 20 amino acids that are secreted from one cell and detected by neighbouring ones.

Experiments revealed that the peptides changed Placozoan behaviour within seconds. Each had a unique effect, which in some cases was very dramatic. The main changes included crinkling, turning, flattening, and internal churning, a behaviour associated with feeding.

“Each peptide can be used individually as a different signal, but the peptides could also be used sequentially or together in different combinations which allows for very high numbers of unique signals between cells,” says Gáspár Jékely from the University of Exeter in the UK.

“This explains how Placozoans can coordinate sophisticated behavioural sequences such as feeding."

Now it makes so much sense why a neuron would conduct an electrochemical signal within the cell but use a diffusion of molecules between cells (the synaptic gap) to communicate that signal...that is because the function of multicellular communication originated with cells in cooperation having evolved such communicative systems. The organ we know of as the nervous system is an evolution of this ancient mechanism.

This reinforces a notion that I have been developing in my head that anything in our bodies or minds that seems purposeful or designed must have originated in a context in which it was free to develop. Obviously for basic neuron inter communication that is not in a macroscopic organism.

 

[sealchan]

I find all of this sort of 'amazing discoveries' to be on par with the amazing Bible Code hysteria of a decade or so ago. You only get the amazing outcomes if you apply the parameters used by the 'discoverers'. I recall reading that someone had used an alteration of the bible code folks and found the 'hidden' message of 'Darwin was right' in the bible.

Also, I am no mathematician, but I did do some googling about this whole 037 issue, and I came across a few rebuttals at various places, to include a snarky response that more or less summarizes my take on these sorts of papers, regardless of who wrote them, from "Graham" at the forum 'Pharyngula':

If you look through a pack of cards, you will be able to find coincidences and patterns. Perhaps all four queens occur together. Perhaps the last ten cards all correspond to prime numbers. The more ingenious you are in the way you look, and the more open you are to different kinds of patterns, the more you will see. The more work you put in, the more you can get out. More formally, the greater the information content of the extraction process, the greater the information content of the result.

Suppose someone decides to throw out the black cards, and just look for patterns among the red ones. It might seem they have just made one choice - red vs black. You could formalize this by saying they have put one bit of information into the extraction process. You would be wrong. They have actually made several choices: They've decided to throw out some cards. (Why? Surely it is more natural to look at them all together? And if we're allowed to throw some out, why not add cards according to some scheme? You could cut the red ones in half for example, to make two red cards for each old one.) Secondly, they've decided to use colour as the criterion for choosing which cards to chuck, when cards have other attributes that could just as well have been used.

It is not possible to evaluate things like this rigourously. You may feel that throwing out some cards is a fairly reasonable thing to do, while cutting some in half is highly contrived. You might then assign just a a couple of bits to a decision to throw, and quite a lot of bits to a decision to cut. Someone else might disagree with your numbers. At any rate, it is crucial to consider all the things you might reasonably have done but didn't, when evaluating a process for extracting patterns. Otherwise, you might unwittingly put more information into the extraction process than you get out as a 'message'.

Bear these considerations in mind when reading the following list of decisions which are used to extract meaning from the genetic code in the paper. There are two major phases: converting (codon,amino acid) pairs to numbers, then looking for patterns in the numbers.

Primary Phase: Making Numbers

1. Decide to throw out the codons and focus on just the amino acids.

2. Decide to map amino acids to numbers, in particular positive integers. Human mathematicians study many kinds of mathematical objects. Graphs, or groups, or sequences of numbers are other possibilities.

3. Decide to disregard the molecular structure of the amino acids and regard them as just an unordered bunch of atoms. There are many numbers that one could derive from the molecular structure using the elements and/or the types of chemical bonds present, or the underlying graph.

4. Decide to focus on the nucleus of the atoms, and ignore the numbers one might derive from the electron shells. (Surely it is a shame not to get a mention of quantum spin into a story like this. Everybody likes a bit of quantum spin.)

5. Decide to ignore the fundamental constituents of the nucleus (the quarks - at least as far we understand the nucleus) and instead focus on the protons and neutrons.

6. Decide to ignore the obvious positive integer related to an atom, that is, the atomic number, which is the number of protons, and also the number of electrons if the atom is not ionized, and instead decide to include the neutrons, despite the fact that this number varies with the isotope. We can choose the most common isotope, and call the result a 'nucleon sum'.

Secondary Phase: Spotting Patterns

7. There's all sorts of things one can do with numbers. Find their prime factors, interpret them as coefficients of a polynomial and look at the roots, interpret them as coefficients of a continued fraction, add them up, subtract them, multiply or divide, compare them to physical or chemical constants, or to numbers that seem important from mathematics, and so on. But we might decide to divide them into two subsets and add them up to form two subsums. Whatever.

8. We've got 20 numbers and there are over a million ways to divide them up, but some ways seem more natural given the genetic code. But wait! We could make more than 20 numbers (or indeed less since some of the numbers are the same). But let's decide to make a few more. Not all amino acids are coded equally. Some might need special treatment. Met and Trp are special, because they are associated with only one codon. Leu, Ser, and Arg are the only ones where the first two letters of the codon can vary. Ser is extraspecial because its codons are not all connected by single substitutions. Ile is special because it is the only one with 3 codons. And Tyr, Cys and Trp are special because their codon shares the first two letters with a Stop codon. And Stop codons are very special. And so on. Anyway, lets decide to make a few more numbers by splitting the Leu, Ser, and Arg numbers into two, according to the first two letters in their codons.

9. There are about 8 million ways to divide the now 23 numbers into two sets. The codons associated with them suggest various more or less contrived possibilities.

Results

For some of these possibilities, it turns out that both subsums are equal and divisible by 37, and 37 is half the nucleon sum of the B groups, apart from proline.

Interpretation

We apologise for the anti-climax.​

If the researchers had used slightly different parameters, their amazing miraculous find would not have been found. It is a product of number manipulation and pattern seeking, nothing more.

For a recent debunked example I think of Richatd Hoagland and Cydonia.