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    • #16761
      searchfortruth
      Participant

      Can someone explain to me how evolution supports the following;
      I am not a biologist or trained scientist so i do not understand .
      How if the code for the protiens required for DNA formation are contained in the DNA/RNA system did the protiens form to begin with? does this question make sense?

      in other words protiens must have come first in order to create the DNA but the code for that protien is contained in the DNA that hasnt been formed yet.

      i guess you could liken it to the chicken or the egg argument.

      thanks,

      Rick

    • #112111
      wbla3335
      Participant

      No one knows. Do a search for "abiogenesis" for some current ideas, but stay away from the creationist sites. They have nothing to contribute to a rational search for truth.

    • #112114
      Rap
      Participant

      The answer is much like the answer to the chicken-and-egg answer, which is that the egg came first, and it was laid by something that was not a chicken. Evolution is continually producing "new" organisms with never-before-seen DNA.

      As far as which came first, the protein or the DNA, early life might have used molecule that reproduced itself, no distinction between protein and DNA. Then maybe a mutation occurred which two forms alternated back and forth. Then maybe a mutation in which the two forms stayed separate, with one more in charge of reproduction than the other, and these two molecules evolved into DNA and proteins. Maybe.

    • #112124
      scottie
      Participant

      Rick
      There are two ways you can address this issue.
      The first is to look at it in a scientific way as you appear to be doing, however it is often mistaken as a chicken and egg argument.

      The reality is that the Cell is the basic unit of life, therefore it was the Cell that had to have been in existence before anything else could have happened, biologically speaking that is.
      Why? Because it is the cell that contains the translation machinery that allows the DNA to code for proteins. It is the cell that contains the machinery that allows for duplication, and so on.

      DNA outside the cell environment is an inert molecule. It will just sit wherever it is, doing nothing but deteriorate into it’s basic constituent parts.

      In very basic terms the cell contains machinery that takes a coded sequence of DNA and Translates that coded sequence to produce a protein. The type of protein made is determined by this coded sequence. This new molecule is then folded in a very precise way into the 3D shape we recognise as a protein. Different proteins have different shapes and coded sequences. Indeed one coded sequence can produce different proteins depending on the way these molecules are folded.

      The question that therefore arises is; How does the DNA get into the cell.

      This is where Real Scientists of the ilk of Craig Venter and his colleges have provided a proof of concept experiment.

      This is what they did and announced in 2010
      http://www.jcvi.org/cms/research/projec … ell/video/

      Spend time with this video which is about one hour in length. The question and answer session at the end is very helpful.
      Hopefully at the end of this instructive video you will appreciate the biological engineering that is needed just to transplant a new chromosome into an existing living cell. This of course does not take account as to how the genetic code underpinning the translation system could have originated.

      Now for the other way.

      You can indulge yourself, as is suggested, and go down the speculative route of “abiogenesis” which has absolutely no scientific foundation. In fact even NASA has recognised that there is no plausible route that these molecules can come together randomly. A fact that the Venter team has demonstrated in a very practical way.

      Abiogenesis is the stuff of fairies at the bottom of the garden. If people wish to research this subject then that is a personal choice.
      However scientific research is another matter.

      To me the beautify in biology is getting an understanding of how life processes work. The more scientists discover the more questions surface.

      scottie

    • #112125
      wbla3335
      Participant
      quote scottie:

      Abiogenesis is the stuff of fairies at the bottom of the garden.

      The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren’t around, so all we can do is surmise. Some of us choose to believe in gods, some don’t.

    • #112134
      Rap
      Participant

      Venter et. al. mention a number of times how his group is the "top down" approach, while those searching for a plausible mechanism for the development of early life (the "bottom up" people) may have something to contribute to each other and will hopefully meet in the middle some day. Ventner et. al. clearly don’t thing that abiogenesis is the "stuff of fairies".

    • #112137
      JackBean
      Participant

      scottie: so, because we can grow plants in garden, no plants are able to grow without us?

    • #112151
      Darby
      Participant

      One of the main theories is that the first main metabolic molecules were RNAs, which can template proteins as well as be active themselves. How you get from such a start to the system seen now hasn’t, so far as I know, been worked out.

    • #112170
      scottie
      Participant

      wbla3335

      quote :

      The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren’t around, so all we can do is surmise. Some of us choose to believe in gods, some don’t.

      You are quite right in that the only alternate to abiogenesis (ie non science)is creation.
      Venter and his team created a new species without any biological precursor.
      This is what is referred to as “a proof of concept.”

      Who is arguing that Venter is a god?
      Certainly not me.
      You continue to confuse religion with science.

      Do you not consider it time to start presenting some science to this forum instead of your religious bias.

      Rap

      quote :

      Venter et. al. mention a number of times how his group is the “top down” approach, while those searching for a plausible mechanism for the development of early life (the “bottom up” people) may have something to contribute to each other and will hopefully meet in the middle some day. Ventner et. al. clearly don’t thing that abiogenesis is the “stuff of fairies”.

      If you read my postings you will realise that the top down approach is precisely what my position is.
      Design is exactly what a top down approach is. Venter and his team designed the new chromosome
      and then engineered a way (using the already existing machinery in yeast) to insert it into the recipient cell thus creating a new species.
      The “stuff of fairies” I refer to, is what exists in peoples imagination and especially so when it is disregards scientific evidence.

      Many people believe in many things, but belief isn’t reality unless it is accompanied by evidence, and there is no evidence that life can arrive from non life. All the scientific evidence shows that life can only come from another life. Venter himself acknowledges that.
      Indeed Darwin himself (maybe unwittingly) acknowledged this fact because he postulated his hypothesis based on common decent, ie one life from another life.

      Jackbean

      quote :

      scottie: so, because we can grow plants in garden, no plants are able to grow without us?

      Sorry I have no idea what your point is? What your statement has to do with my posting is really beyond me.

      However we have been down this road before, so perhaps a refresher might be in order.
      The Ribosome is the translation system for the manufacturing of proteins.
      This process starts with Transcription.
      This is the first step in decoding a cell’s genetic information. During transcription, Enzymes called RNA polymerases build RNA molecules that are complementary to a portion of one strand of the DNA double helix.
      Now what is an enzyme?
      Guess what? It is a protein.

      This basic refresher tell us that a Protein is required at the start of a process to make (guess what?)another Protein.
      That is why I argue that the Cell is the basic unit of life. I really don’t see what the difficulty is in understanding such a simple concept.
      Unless of course some pre conceived philosophy is coming in the way.

    • #112171
      scottie
      Participant

      Darby

      quote :

      One of the main theories is that the first main metabolic molecules were RNAs, which can template proteins as well as be active themselves. How you get from such a start to the system seen now hasn’t, so far as I know, been worked out.

      I agree with you about the RNA world having been one of the main theories.
      In 1968 Sir Francis Crick argued that RNA must have been the first genetic molecule. He went on to suggest that RNA, besides acting as a template, might also act as an enzyme and, in so doing, catalyze its own self-replication.

      The problem now is that, as knowledge has accumulated, his idea has become obsolete.
      Challenges to this idea have been many and various (I refer not to any creationist literature).
      NASA has discounted it.
      One of the latest studies published in March this year can be found here:-
      http://news.illinois.edu/news/12/0312ri … olles.html
      Study of ribosome evolution challenges RNA world hypothesis

      Here is what the lead researcher had to say

      quote :

      “This is the crucial piece of the puzzle,” Caetano-Anollés said. “If the evolutionary buildup of ribosomal proteins and RNA and the interactions between them occurred gradually, step-by-step, the origin of the ribosome cannot be the product of an RNA world. Instead, it must be the product of a ribonucleoprotein world, an ancient world that resembles our own. It appears the basic building blocks of the machinery of the cell have always been the same from the beginning of life to the present: evolving and interacting proteins and RNA molecules.

       

    • #112172
      wbla3335
      Participant
      quote scottie:

      Venter and his team created a new species without any biological precursor.
      This is what is referred to as “a proof of concept.”

      Venter has not created life. No "proof of concept" here.

      quote scottie:

      You continue to confuse religion with science.

      Not me. Look in a mirror.

      quote scottie:

      Do you not consider it time to start presenting some science to this forum instead of your religious bias.

      I have no religious bias. Look in a mirror.

      quote scottie:

      Many people believe in many things, but belief isn’t reality unless it is accompanied by evidence, and there is no evidence that life can arrive from non life.

      And there’s no evidence that life was created by a supernatural entity. As I’ve already said (twice) before, no one knows how life on Earth, or in the universe, began. If you believe that life on Earth was created by some advanced being (which no one can discount), then how did this advanced being originate? Pushing back creation to earlier sources must have an end (i.e beginning), and that end can only be abiogenesis or creation by a supernatural entity.

      Your continual appeals to your faith in science are becoming tiresome. You have done nothing in your posts but misunderstand or misinterpret the findings of science. If you do not wish to accept the findings of science, then that’s OK. Just don’t be a hypocrite. All science has been able to do, all it is able to do, is to try and test what might have been possible. No more. If you feel that science has found evidence that life was created by a supernatural entity, please present it. Be specific.

    • #112184
      JackBean
      Participant
      quote scottie:

      Venter and his team created a new species without any biological precursor.
      This is what is referred to as “a proof of concept.”

      Seriously? And I thought they used bacteria into which they put artifical DNA. However, still molecule, which is found everywhere around us. Thus, still nothing new.

      And even if they have created something new, that doesn’t mean it had to happen that way in nature. Just because we are able to grow trees in gardens, does that mean they do not grow in wildness? Only because we can grow them artificially, they cannot grow naturally (without any help)? After we will be able to produce meat in Petri dishes, will that mean, that no meat is produced by Nature?

    • #112186
      Rap
      Participant

      Look, lets be clear about what Ventner et. al. have done. They have taken the DNA from one species (A), tacked on some non-functional additions to the DNA to make it different, but functionally the same. They then inserted that DNA into the cell of a closely related species (B), and that B cell was transformed into a type A cell, functionally. If the DNA is like the "computer program" for the cell, all they did was add some comment lines to the code and insert it into a similar cell, and that B cell transformed to an A cell, functionally. They did not create nor engineer a new DNA in the functional sense. This is not to dismiss what they have done, because their next step is to start fiddling with the functional part of the DNA in order to learn how the cell works. How to understand the code rather than just read the code. Sure, they know every base pair in the DNA and what proteins are encoded by that DNA, but they don’t fully understand the chemistry and mechanics of the cell that follows from this DNA and the proteins it creates.

      Second of all, just because no evidence of life arising from non-life has been found does not constitute a proof that none exists. Typical "creationist" logic.

      I mean, I believe in God, and I have faith that he created the universe, I just don’t know how, and I don’t ever expect to. The evidence for evolution and the logic of evolution is overwhelming, so I think (not believe!) that it is true, it’s a small step on the path to understanding God’s universe. Anyone frantically trying to disprove evolution because it denies God is arrogant and has little faith. Anyone who believes evolution denies God is also arrogant and has little faith. When it comes to life, we may be like cave men trying to understand what makes the sun go round. Oh, its Apollo, the sun god. No it isn’t. Yes it is. It’s such a tired, tired argument.

    • #112191
      Forests
      Participant
      quote :

      The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren’t around, so all we can do is surmise. Some of us choose to believe in gods, some don’t.

      That is not fully true becuase there is also panspermia, see for example the book Intelligent Universe by Fred Hoyle. However panspermia does not need to completely replace abiogenesis, a bit of both may explain it.

    • #112192
      wbla3335
      Participant

      Panspermia is a mechanism for the dissemination of life, not its origin. Francis Crick was a proponent of panspermia for life on Earth.

    • #112193
      scottie
      Participant

      Jackbean

      It is Venter’s claim that his team “created a new species without any biological precursor.”
      It was he that referred to this as a “proof of concept”

      If you have an argument with that, it is not with me but with real biologists and engineers.

      Now your comment

      quote :

      And even if they have created something new, that doesn’t mean it had to happen that way in nature.

      They did create something new, and the “proof of concept” was the fact that this occurred by direct intervention from an outside source (his team). My argument is that this is the way species arrive and Venter has demonstrated that.

      Now your argument is

      quote :

      “that doesn’t mean it had to happen that way in nature.”

      Well ok if that is the case, put out your own scenario as to how it happened. At the moment you are simply relying on a belief that nature can do this randomly and without direction.
      Many brilliant minds have tried and they can’t even agree amongst themselves.
      So please, show how that can happen and we are in a serious scientific discussion.
      If you can’t then your view is based, not on science but on a philosophy.

      What I say however is; don’t conflate belief with science, because if you do then you are obliged to prove your belief scientifically.
      Everyone is entitled to believe whatever they wish and there is nothing wrong with that. After all Wbla3335
      believes in abiogenesis. Of course its not science, but nothing wrong with that. 🙂

      He is also having great trouble in understanding the difference between creating life and creating a species.
      Science by it very nature can’t explain how life was created because science is constrained by natural laws.
      Life is not a physio/chemical entity that can be explained by natural laws.
      He also is having trouble understanding that, as I of course have in believing in fairies at the bottom of the garden. 🙂

      Science however can and has explained and indeed demonstrated, how a new species without any biological precursor can be created. It is not a natural way because it had to be engineered by minds.

      My argument is and has been that species did not arrive by the due process of natural laws.
      Species have only arrived by some outside intervention.

      Venter and his team have demonstrated this by his proof of concept bit of engineering.

      Has anyone been able to provide a proof of concept of the natural processes?
      The answer is a resounding No.

      The more the science in cell biology is uncovered the more it demonstrates that natural processes could not have originated it. It had to have been engineered.

      I will in my next post on the other thread point to the latest information on what constitutes a gene,
      which take this point even further.

    • #112195
      JackBean
      Participant
      quote Forests:

      quote :

      The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren’t around, so all we can do is surmise. Some of us choose to believe in gods, some don’t.

      That is not fully true becuase there is also panspermia, see for example the book Intelligent Universe by Fred Hoyle. However panspermia does not need to completely replace abiogenesis, a bit of both may explain it.

      And where does the panspermic life come from?

    • #112196
      JackBean
      Participant

      I’m sure you will show me, where Venter said that this is proof of creation by God. Or is another example of your favourite quote mining?

    • #112197
      wbla3335
      Participant
      quote scottie:

      I will in my next post on the other thread point to the latest information on what constitutes a gene, which take this point even further.

      You needn’t bother. No one here is particularly interested in your inability to understand science or your ability to misinterpret it. Believe in your god if you want. Believe that science supports your belief if you want. We have continually tried to show you how your "evidence" is misguided, but you’re not listening. A deaf man cannot hear. A blind man cannot see. A closed mind can be opened, but only if it wants to be opened. Yours does not.

    • #112200
      Forests
      Participant
      quote JackBean:

      quote Forests:

      quote :

      The only alternative to abiogenesis is creation, which is not exactly free of fairies. As I said, no one knows. The documentary crews weren’t around, so all we can do is surmise. Some of us choose to believe in gods, some don’t.

      That is not fully true becuase there is also panspermia, see for example the book Intelligent Universe by Fred Hoyle. However panspermia does not need to completely replace abiogenesis, a bit of both may explain it.

      And where does the panspermic life come from?

      there is no origin for life, life has always existed but to answer your question it came from other planets. most scientists agree the big bang was not the start of everything only the early development of this Universe. perhaps there are an infinite amount of multiverses.

      if we just equate existence with life then you will see the whole debate about God/s is futile. if life has always existed then where is the room for any external deity? how could an external God create anything if something has always existed? something has always existed so how could there be any external deity? even if god/s did exist then what came before the Gods?? you start thinking about it and it does not add up!! something has always existed and there is no reason to believe was a religious God.

      having read the above someone will probably call me an atheist etc but i am not, in my opinion i believe the evidence supports pantheism. if we equate god with the universe itself ie in all matter then there is no external deity, god becomes the universe and that best fits the evidence in my view but it is still a philosophical view of the evidence and I cant go about proving it to anyone.

    • #112205
      Rap
      Participant

      Did Ventner et. al. invent a new species? They took the DNA from one species, added some non-functional "comment lines", removed the DNA from a closely related species, inserted the DNA-with-comment-lines into it, and the new cell was viable, functionally the same as the cell it came from.

      If the original cell has the capacity to sexually reproduce, can it sexually reproduce with the new cell? If so, its not a new species. If it cannot, then it is a new species. If it does not sexually reproduce, what makes it a new species?

    • #112337
      scottie
      Participant

      Jackbean

      quote :

      I’m sure you will show me, where Venter said that this is proof of creation by God. Or is another example of your favourite quote mining?

      Where have I stated

      quote :

      Venter said that this is proof of creation by God

      Is raising this sort of fabrication, the only way you can debate?

      Maybe your hope is that no one will actually read my posts and simply rely on your “creative quote mining” 🙂

      Come come now, I was really hoping you could do better that this.

      Rap

      quote :

      Did Ventner et. al. invent a new species? They took the DNA from one species, added some non-functional “comment lines”, removed the DNA from a closely related species, inserted the DNA-with-comment-lines into it, and the new cell was viable, functionally the same as the cell it came from.

      You are not accurate in your post. May I offer some corrections.
      The source DNA was chemically synthesised.
      You will find this paper from Venter’s team helpful.
      http://www.ncbi.nlm.nih.gov/nuccore/296455217

      Their comment reads
      The genome, which was designed based on Genbank Accession Number
      CP001668 (Mycoplasma mycoides subs. capri str. GM12), was assembled
      from chemically synthesized oligonucleotides. The sequenced genome
      was isolated from a yeast clone. The sequenced clone is
      sMmYCp235-1.

      This synthetic genome contains all but 14 of the genes of wild type
      Mycoplasma mycoides subspecies capri strain GM12. Among the genes
      deleted from the genome are components of the ABC glycerol
      transporter operon gtsABCD. These genes are involved in the
      production of hydrogen peroxide, which is believed to be the
      principal virulence factor of the mycoides group of mycoplasmas .
      The genome also contains added watermark sequences for
      identification of the genome as synthetic and also antibiotic
      resistance markers to allow for selection. Overlapping cassettes of
      1080 were assembled from chemically synthesized oligonucleotides.
      The complete synthetic genome was assembled by transformation
      associated recombination (TAR) cloning in the yeast Saccharomyces
      cerevisiae, then isolated and sequenced. A clone with the correct
      sequence was identified and transplanted in Mycoplama capricolum
      subspecies capricolum recipient cells in which the restriction
      modification system had been inactivated. This synthetic M. mycoide
      genome can be isolated for future work.

      The company that provided the initial synthesis was Blue Heron.
      http://www.blueheronbio.com/Services/Ge … hesis.aspx

      I think you will find that the “old DNA” was not removed. It couldn’t because the cell would have died.
      The new DNA was inserted, and to prevent rejection the “restriction modification system” was inactivated.
      If you listen to the video on Venter’s site you will get a good idea as to what they actually did.
      As to your comment about

      quote :

      If the original cell has the capacity to sexually reproduce, can it sexually reproduce with the new cell? If so, its not a new species. If it cannot, then it is a new species. If it does not sexually reproduce, what makes it a new species?

      Firstly, your question is simply hypothetical.
      The new cell does not reproduce sexually.

      Venter describes it as a new species without a biological ancestor.
      I would suggest you email him and ask him why he considers it a new species.

    • #112338
      Rap
      Participant

      To scottie – being a computer programmer, I don’t draw a distinction between a file containing code and another file with the identical code, as far as programming goes. That’s what I meant by "taken from". Thanks for the quote – correct me if I am wrong, but, as I understand it, the constructed DNA is identical to the DNA of the first organism, except for a few non-vital deletions, and then an addition of a non-functional length of DNA.

      Regarding whether it is a new species, I guess I don’t know what constitutes a new species for an asexual organism. Any ideas? Maybe I _should_ email him.

    • #112376
      scottie
      Participant

      Rap
      Sorry for the delay, I have only limited time to devote to this forum.
      Thanks for clearing up my misunderstanding. Good to know your are a computer programmer. I have done some myself, mainly on 4GL relational database stuff
      As far as the species point is concerned, the Venter Institute has a FAQ which I think helps.
      http://www.jcvi.org/cms/research/projec … -cell/faq/
      They produced a clone of an existing genome and removed some 14 genes.

      quote :

      The syntheticM. mycoides organism has 14 genes deleted or inactivated, including genes that are predicted to be critical to virulence.

      Question 9 of the FAQ provides some more information for you.
      As far as species categorisation, this site may help.
      http://www.mansfield.ohio-state.edu/~sa … ol3010.htm

      On a general point as to whether this is a completely new genome.
      The answer is no, as this is just a first stage in that process.
      This proof of principle or concept was to determine whether it was possible to create a genome and insert it into a cell. The best way was to construct a genome that was a copy of an existing one which they knew would work. That process took them 15 years.
      The next stage then is to commence going down the road of constructing a new genome.

      Incidentally the synthetic genome is somewhat different from that of the original even apart from the deletions. What you have referred to as the “non functional” lengths of DNA do actually actually function, however because the proteins produced are just fragments they are effectively neutral to the cellular production. They were able to create a new code for these "non function" lengths because there is a lot of redundant space in the triplet codon for 20 amino acids. There are 64 codons available and they took advantage of the additional 44 that could be used.

      You will find the video of the press conference answers a lot of your questions. In particular the question and answer session from around 32 minutes in.
      http://www.jcvi.org/cms/research/projec … ell/video/

      Hope this helps

    • #112379
      JackBean
      Participant

      What else is this?

      Re: question for evolutionary biologist.

      Postby scottie » Tue Aug 28, 2012 1:23 pm
      Jackbean

      It is Venter’s claim that his team “created a new species without any biological precursor.”
      It was he that referred to this as a “proof of concept”

    • #112380
      JackBean
      Participant

      and BTW if you take DNA from some organism and synthesise exactly the same chemically, you will not find any difference. Thus the chemical synthesis of the DNA (which was BTW assembled by bacteria) doesn’t mean anything.

    • #112382
      scottie
      Participant

      And so your point is what?

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