DNA built from "scratch"?

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DNA built from "scratch"?

#1  Postby truelgbt » Sep 19, 2018 9:16 pm

"Scientists have long been able to make specific changes in the DNA code. Now, they're taking the more radical step of starting over, and building redesigned life forms from scratch. Boeke, a researcher at New York University, directs an international team of 11 labs on four continents working to "rewrite" the yeast genome, following a detailed plan they published in March.

Their work is part of a bold and controversial pursuit aimed at creating custom-made DNA codes to be inserted into living cells to change how they function, or even provide a treatment for diseases. It could also someday help give scientists the profound and unsettling ability to create entirely new organisms."

Read more at: https://phys.org/news/2017-07-scientist ... t.html#jCp

When I first read the title, I thought "WHOA".
But then I read that:
1) They are still using living material (yeast) as opposed to purely from "scratch", which would be nonliving material, not living.
2) They are "rewriting" the yeast genome, i.e. modifying it, not building an entire genome from "scratch".
3) Their "custom made" DNA codes are undoubtedly sourced from the DNA of living organisms.

Firstly, "scratch" may mean different things to different people. However, IMHO, "scratch" means just that, from material/molecules that are not DNA nor from the products of DNA. No methane, no ammonia, no nucleic acids, no organic chemical compounds, etc..

This reminds me of my disappointed reaction to the Miller-Urey experiment which also started by introducing products of DNA (methane, ammonia) which, IMHO, is almost equivalent to "stacking the deck" or "planting evidence" into the experiment. Yes, I understand they were trying to mimic the prehistoric environment of methane from volcanoes, for example, but studies show that about 95% of methane on earth is due to life forms, i.e. products of DNA, so methane itself can, and is, largely considered to be a product of DNA.

It pees me off when article titles seem to be purposely worded to get our attention but are deceiving too. Are they that desperate to get our attention? What do you think?
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Re: DNA built from "scratch"?

#2  Postby laklak » Sep 19, 2018 10:22 pm

Well, I make most of my food from scratch. Take cornbread, for example. I don't grow or grind the corn or wheat flour, I don't milk the cows or churn the butter, I don't have a lab in the garage to make baking powder, and I don't keep chickens for the eggs. But it's still "scratch cornbread".
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Re: DNA built from "scratch"?

#3  Postby newolder » Sep 19, 2018 10:27 pm

To make anything from scratch, one must first invent the Universe. Sagan-ish
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Re: DNA built from "scratch"?

#4  Postby Rumraket » Sep 21, 2018 9:47 am

truelgbt wrote:This reminds me of my disappointed reaction to the Miller-Urey experiment which also started by introducing products of DNA (methane, ammonia) which, IMHO, is almost equivalent to "stacking the deck" or "planting evidence" into the experiment. Yes, I understand they were trying to mimic the prehistoric environment of methane from volcanoes, for example, but studies show that about 95% of methane on earth is due to life forms, i.e. products of DNA, so methane itself can, and is, largely considered to be a product of DNA.

This makes no sense at all. There are clearly nonbiological sources of methane. You even write yourself that 95% of extant methane is produced by life, but then 5% isn't. So using methane can't be stacking the deck in any way.

So going back before the origin of life, there was volcanoes, and they would have produced some methane.
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Re: DNA built from "scratch"?

#5  Postby theropod » Sep 21, 2018 6:19 pm

I think we just need to go ahead and build a replicator, and then we can convert energy into any material we choose. We could produce whole living organisms, or any part thereof. Then, and only then, would science denialist semi-accept that life is no more than chemistry. Maybe. Sort of. Almost.

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Re: DNA built from "scratch"?

#6  Postby Destroyer » Sep 21, 2018 9:33 pm

theropod wrote:I think we just need to go ahead and build a replicator, and then we can convert energy into any material we choose. We could produce whole living organisms, or any part thereof. Then, and only then, would science denialist semi-accept that life is no more than chemistry. Maybe. Sort of. Almost.

RS

Well, I am certainly no science denialist: I implicitly trust that the physical universe functions independently and is not reducible to any God. However, I also implicitly trust that chemistry is not the source of life; despite the evidence which indicates that it IS... What that means is that despite my rejection of God being the source of the physical I am nevertheless absolutely certain that life is His property.
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Re: DNA built from "scratch"?

#7  Postby Calilasseia » Sep 21, 2018 10:21 pm

The 12th century is that way ...
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Re: DNA built from "scratch"?

#8  Postby Blackadder » Sep 22, 2018 7:54 pm

Destroyer wrote:
theropod wrote:I think we just need to go ahead and build a replicator, and then we can convert energy into any material we choose. We could produce whole living organisms, or any part thereof. Then, and only then, would science denialist semi-accept that life is no more than chemistry. Maybe. Sort of. Almost.

RS

Well, I am certainly no science denialist: I implicitly trust that the physical universe functions independently and is not reducible to any God. However, I also implicitly trust that chemistry is not the source of life; despite the evidence which indicates that it IS... What that means is that despite my rejection of God being the source of the physical I am nevertheless absolutely certain that life is His property.


Which god? There are people who are abolutely convinced, even unto the red font, bolded and italicised, that life is the property of Lord Brahma. And they are in possession of exactly the same evidence for their convictions as you are.
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Re: DNA built from "scratch"?

#9  Postby truelgbt » Sep 23, 2018 8:38 am

Rumraket wrote:
truelgbt wrote:This reminds me of my disappointed reaction to the Miller-Urey experiment which also started by introducing products of DNA (methane, ammonia) which, IMHO, is almost equivalent to "stacking the deck" or "planting evidence" into the experiment. Yes, I understand they were trying to mimic the prehistoric environment of methane from volcanoes, for example, but studies show that about 95% of methane on earth is due to life forms, i.e. products of DNA, so methane itself can, and is, largely considered to be a product of DNA.

This makes no sense at all. There are clearly nonbiological sources of methane. You even write yourself that 95% of extant methane is produced by life, but then 5% isn't. So using methane can't be stacking the deck in any way.

So going back before the origin of life, there was volcanoes, and they would have produced some methane.


Methane and ammonia are not just products of volcanoes; they are also produced by bacteria in much larger quantities than volcanoes by a ratio of 95:5. Therefore methane and ammonia are not just associated with DNA, they are considered products of DNA i.e. products of life, not just by me but the scientific community in general. You will not find any article denying that methane and ammonia are associated with bacteria. They are.

The higher standard for performing an experiment to generate 'life' in the lab is to exclude ANYTHING associated, even remotely, with life. No methane, no ammonia, etc. But that's just me. I prefer a higher standard.

The lower standard, IMHO, is to introduce all kinds of products of life into the experiment such as methane, ammonia, organic materials, etc. So, for example, if you are trying to generate life in an experiment and introduce materials already produced by life into the experiment, what have you demonstrated? In other words, if your experiment begins with products of DNA, and your experiment ends with products of DNA, what have you demonstrated?

I am not trying to be difficult but just asking the difficult questions that everybody should be asking.
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Re: DNA built from "scratch"?

#10  Postby Fenrir » Sep 23, 2018 9:33 am

What rubbish.

Excluding any molecule known to be associated with life would be self defeating, as it would, you know, remove all molecules associated with life, making the biogenesis of said life rather problemmatic.

If molecules like ammonia and methane are known to occur abiogenically and concentrate in places with other things life needs, like liquid water and energy, then their incorporation into origin of life research is totally justified.

As it happens there are places where abiogenic ammonia and methane occur in high concentrations in liquid water with high temperature and a plethora of other exotic molecules. Maybe we should be looking for plausible models in such places. Oh, silly me, we are.

BTW, these are not remotely difficult questions and they were indeed asked and answered long ago.
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Re: DNA built from "scratch"?

#11  Postby Destroyer » Sep 23, 2018 4:12 pm

Blackadder wrote:
Destroyer wrote:
theropod wrote:I think we just need to go ahead and build a replicator, and then we can convert energy into any material we choose. We could produce whole living organisms, or any part thereof. Then, and only then, would science denialist semi-accept that life is no more than chemistry. Maybe. Sort of. Almost.

RS

Well, I am certainly no science denialist: I implicitly trust that the physical universe functions independently and is not reducible to any God. However, I also implicitly trust that chemistry is not the source of life; despite the evidence which indicates that it IS... What that means is that despite my rejection of God being the source of the physical I am nevertheless absolutely certain that life is His property.


Which god? There are people who are abolutely convinced, even unto the red font, bolded and italicised, that life is the property of Lord Brahma. And they are in possession of exactly the same evidence for their convictions as you are.

There are others who possess the same evidence of God as I?! You know not what you speak.
There are absolutely no others who have evidence and can reason that God is non-existent and yet simultaneously existent. In other words, all others who believe in God are convinced that He is the legitimate creator of this physical universe: they are compelled to have faith in supernatural causation. I categorically reject any supernatural causation or involvement with this universe; and, yet, I still insist and can logically reason God to be intimately associated with this universe.
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Re: DNA built from "scratch"?

#12  Postby laklak » Sep 23, 2018 5:06 pm

Good for you.
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Re: DNA built from "scratch"?

#13  Postby Destroyer » Sep 23, 2018 5:37 pm

laklak wrote:Good for you.

It may seem to be good for me - assuming that what I have said could in fact be validated - but in actuality it is a curse.
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Re: DNA built from "scratch"?

#14  Postby truelgbt » Sep 24, 2018 2:40 am

Fenrir wrote:Excluding any molecule known to be associated with life would be self defeating, as it would, you know, remove all molecules associated with life, making the biogenesis of said life rather problemmatic.


Methane and ammonia are not just "molecules" associated with life like water or nitrogen or hydrogen but products directly associated with living things like bacteria, thus methane and ammonia are actually byproducts of DNA, not just water molecules which all of life needs, for example.

You are confusing two different things:
1) molecules needed for life (e.g. h20) and...
2) actual byproducts of DNA like methane and ammonia.

If you want to add molecules needed to sustain life (e.g. h20) to an 'origin of life' experiment, I am in total agreement with it.

However, add an actual byproduct or product of life itself (methane or ammonia), and that is called "stacking the deck' or "planting evidence" in my book and is a very UNconvincing experiment. Be convinced if you want, as I'm sure many people such as yourself are, but I need a hell of a lot more to convince me. I remain skeptical of such so called 'experiments' which use products of DNA itself.

Who knows, maybe next time those clowns might as well just introduce some DNA and see what happens. It'll undoubtedly garner lots of accolades, lol.
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Re: DNA built from "scratch"?

#15  Postby Macdoc » Sep 24, 2018 2:58 am

However, add an actual byproduct or product of life itself (methane or ammonia), methane and ammonia


Um there are non living sources for methane

But detecting lots of methane on Mars would not be convincing evidence of life by any stretch. The gas can also be produced by abiotic processes, such as the degradation of interplanetary dust particles by ultraviolet light and interactions between water and rocks.



§3. FROZEN AMMONIA (NH3)

Submillimeter observations have shown that NH3 is one of the most abundant gas-phase molecules in dense clouds (see Cesaroni et al. 1994) where models suggest that NH3 should be formed in the gas phase (see Scott, Freeman, & McEwen 1997). At the low temperatures typical of dense clouds (T<50 K), NH3 should freeze onto grains very efficiently (Sandford & Allamandola 1993). The presence of solid state NH3 is implied by the fact that gas phase NH3 is enhanced in warmer cloud regions, where it is posited to be subliming from ices (see Cesaroni et al. 1994).

https://en.wikipedia.org/wiki/Hypotheti ... ochemistry

http://iopscience.iop.org/article/10.10 ... .text.html

If you had some basic science education and reading you would know these things and not face plant so frequently. :coffee:
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Re: DNA built from "scratch"?

#16  Postby Fenrir » Sep 24, 2018 3:27 am

truelgbt wrote:
Fenrir wrote:Excluding any molecule known to be associated with life would be self defeating, as it would, you know, remove all molecules associated with life, making the biogenesis of said life rather problemmatic.


Methane and ammonia are not just "molecules" associated with life like water or nitrogen or hydrogen but products directly associated with living things like bacteria, thus methane and ammonia are actually byproducts of DNA, not just water molecules which all of life needs, for example.



Soooo

Black smokers are products of DNA now?

Saturn and Jupiter are products of DNA? Sexual reproduction or simple fission? The mind boggles.

:scratch:
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Re: DNA built from "scratch"?

#17  Postby truelgbt » Sep 27, 2018 1:02 am

In my opening statement I said methane and ammonia have nonliving sources. But methane and ammonia also have living sources. By a 95:5 ratio no less. Bacterial fermentation is listed at the top as a source of methane along with volcanoes at the bottom.

Introducing any substance that is a product or byproduct of DNA is clearly a big no-no for origin-of-life experiments.
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Re: DNA built from "scratch"?

#18  Postby Fenrir » Sep 27, 2018 1:19 am

Logic!

Yep, you said it.

No-one can take that away from you.
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Re: DNA built from "scratch"?

#19  Postby laklak » Sep 27, 2018 1:22 am

truelgbt wrote:

Introducing any substance that is a product or byproduct of DNA is clearly a big no-no for origin-of-life experiments.


It's clearly not. If it exists it can be used. Fail. Try again.
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Re: DNA built from "scratch"?

#20  Postby Macdoc » Sep 27, 2018 1:33 am

ain't it just fun having a chew toy ...

Image

ah ..this one is better

Image

evo deniers are soooo tasty :coffee:
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